U.S. patent application number 13/450886 was filed with the patent office on 2012-10-04 for rnai modulation of apob and uses thereof.
This patent application is currently assigned to ALNYLAM PHARMACEUTICALS, INC.. Invention is credited to Sayda Elbashir, Philipp Hadwiger, Juergen Soutschek, Hans-Peter Vornlocher.
Application Number | 20120252872 13/450886 |
Document ID | / |
Family ID | 36119510 |
Filed Date | 2012-10-04 |
United States Patent
Application |
20120252872 |
Kind Code |
A1 |
Soutschek; Juergen ; et
al. |
October 4, 2012 |
RNAi Modulation of APOB and Uses Thereof
Abstract
The invention relates to compositions and methods for modulating
the expression of apolipoprotein B, and more particularly to the
downregulation of apolipoprotein B by chemically modified
oligonucleotides.
Inventors: |
Soutschek; Juergen;
(Kasendorf, DE) ; Vornlocher; Hans-Peter;
(Bayreuth, DE) ; Hadwiger; Philipp;
(Altenkunstadt, DE) ; Elbashir; Sayda; (Cambridge,
MA) |
Assignee: |
ALNYLAM PHARMACEUTICALS,
INC.
Cambridge
MA
|
Family ID: |
36119510 |
Appl. No.: |
13/450886 |
Filed: |
April 19, 2012 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12728139 |
Mar 19, 2010 |
8188061 |
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13450886 |
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12400744 |
Mar 9, 2009 |
7723317 |
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12728139 |
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11235385 |
Sep 26, 2005 |
7528118 |
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12400744 |
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60613141 |
Sep 24, 2004 |
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Current U.S.
Class: |
514/44A ;
536/24.5 |
Current CPC
Class: |
A61P 9/10 20180101; A61P
7/02 20180101; A61K 31/718 20130101; A61P 3/00 20180101; A61K
31/7105 20130101; C12N 15/113 20130101; C12N 2310/14 20130101; A61P
3/06 20180101; C12N 2310/3515 20130101; A61P 9/00 20180101; C12N
2310/315 20130101; C12N 2310/321 20130101; C12N 2310/321 20130101;
C12N 2310/3521 20130101 |
Class at
Publication: |
514/44.A ;
536/24.5 |
International
Class: |
A61K 31/713 20060101
A61K031/713; A61P 3/06 20060101 A61P003/06; A61P 9/10 20060101
A61P009/10; A61P 9/00 20060101 A61P009/00; A61P 7/02 20060101
A61P007/02; C07H 21/02 20060101 C07H021/02; A61P 3/00 20060101
A61P003/00 |
Claims
1. An iRNA agent comprising a sense strand and an antisense strand,
wherein said sense strand comprises a first sequence and said
antisense strand comprises a second sequence, wherein said first
sequence is complementary to said second sequence, wherein said
first sequence is complementary to a segment of an Apolipoprotein B
(ApoB) mRNA, and wherein each strand of said iRNA agent is between
15 and 30 base pairs in length.
2. The iRNA agent of claim 1, further comprising a non-nucleotide
moiety.
3. The iRNA agent of claim 1, further comprising a phosphorothioate
linkage.
4. The iRNA agent of claim 3, wherein said iRNA agent comprises a
phosphorothioate at the first and second internucleotide linkage at
the 3' end of the antisense strand.
5. The iRNA agent of claim 3, wherein said iRNA agent comprises a
phosphorothioate at the first internucleotide linkage at the 3' end
of the sense strand.
6. The iRNA agent of claim 1, further comprising a 2'-modified
nucleotide.
7. The iRNA agent of claim 6, wherein the 2'-modification is chosen
from the group of: 2'-deoxy, 2'-deoxy-2'-fluoro, 2'-O-methyl,
2'-O-methoxyethyl (2'-O-MOE), 2'-O-aminopropyl (2'-O-AP),
2'-O-dimethylaminoethyl (2'-O-DMAOE), 2'-dimethylaminopropyl
(2'-O-DMAP), 2'-O-dimethylaminoethyloxyethyl (2'-O-DMAEOE), and
2'-O--N-methylacetamido (2'-O-NMA).
8. The iRNA agent of claim 6, further comprising: at least one
5'-uridine-adenine-3' (5'-UA-3') dinucleotide wherein the uridine
is a 2'-modified nucleotide; at least one 5'-uridine-guanine-3'
(5'-UG-3') dinucleotide, wherein the 5'-uridine is a 2'-modified
nucleotide; at least one 5'-cytidine-adenine-3' (5'-CA-3')
dinucleotide, wherein the 5'-cytidine is a 2'-modified nucleotide;
or at least one 5'-uridine-uridine-3' (5'-UU-3') dinucleotide,
wherein the 5'-uridine is a 2'-modified nucleotide.
9. The iRNA agent of claim 8, wherein the 5'-most pyrimidines in
all occurrences of sequence motif 5'-UA-3', 5'-CA-3', 5'-UU-3', and
5'-UG-3' on the antisense strand are 2'-modified nucleotides.
10. The iRNA agent of claim 1, wherein the first sequence is
selected from the sense strand sequences shown in Tables 1, 3, 10,
or 11.
11. The iRNA agent of claim 1, wherein the second sequence is
selected from the antisense strand sequences shown in Tables 1, 3,
10, or 11.
12. The iRNA agent of claim 1, wherein a 5'-end of said iRNA agent
comprises an adenosine, cytidine, guanosine, thymidine, or
uridine.
13. The iRNA agent of claim 1, further comprising a nucleotide
overhang having 1 to 4 nucleotides.
14. The iRNA agent of claim 13, wherein the nucleotide overhang has
2 or 3 unpaired nucleotides.
15. The iRNA agent of claim 13, wherein the nucleotide overhang is
at the 3'-end of the antisense strand of the iRNA agent.
16. The iRNA agent of claim 1, further comprising a cholesterol
moiety.
17. The iRNA agent of claim 16, wherein the cholesterol moiety is
conjugated to the 3'-end of the sense strand of the iRNA agent.
18. The iRNA agent of claim 1, wherein said iRNA agent reduces the
amount of ApoB mRNA present in cultured mouse cells of hepatic
origin by an amount greater than a control iRNA agent.
19. The iRNA agent of claim 1, wherein the agent reduces the amount
of ApoB mRNA in cultured human HepG2 cells after incubation with
the agent by more than 50% compared to cells that have not been
incubated with the agent, or reduces the amount of ApoB protein
secreted into cell culture supernatant by more than 50% compared to
a control.
20. A method for reducing the expression levels of ApoB in a
subject, further comprising the step of administering the iRNA
agent of claim 1 to said subject.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional application of U.S. patent
application Ser. No. 12/728,139, filed Mar. 19, 2010, which is a
divisional application of U.S. patent application Ser. No.
12/400,744, filed Mar. 9, 2009, now issued as U.S. Pat. No.
7,723,317, which is a divisional application of U.S. patent
application Ser. No. 11/235,385, filed Sep. 26, 2005, now issued as
U.S. Pat. No. 7,528,118, and which claims priority to U.S.
Provisional Application Ser. No. 60/613,141, filed Sep. 24, 2004;
each of which is incorporated herein by reference in its
entirety.
SEQUENCE LISTING
[0002] In accordance with 37 C.F.R. .sctn.1.821(c), this
application is filed with an electronically submitted Sequence
Listing in ASCII text format (68 kb), entitled
"16562_US_Sequence_Listing," created on Mar. 19, 2010. This
Sequence Listing is hereby incorporated by reference, in its
entirety and for all purposes.
TECHNICAL FIELD
[0003] The invention relates to compositions and methods for
modulating the expression of apolipoprotein B, and more
particularly to the downregulation of apolipoprotein B by
oligonucleotides, e.g., chemically modified oligonucleotides.
BACKGROUND
[0004] RNA interference or "RNAi" is a term initially coined by
Fire and co-workers to describe the observation that
double-stranded RNA (dsRNA) can block gene expression when it is
introduced into worms (Fire et al., Nature 391:806-811, 1998).
Short dsRNA directs gene-specific, post-transcriptional silencing
in many organisms, including vertebrates, and has provided a new
tool for studying gene function.
[0005] Lipoproteins consist of acylglycerols and cholesteryl esters
surrounded by an amphiphilic coating of protein, phospholipid and
cholesterol. The protein components of lipoproteins are known as
apolipoproteins, and at least nine apolipoproteins exist in humans.
Apolipoprotein B (ApoB) is found in various classes of
lipoproteins: chylomicrons, very low density lipoproteins (VLDL),
intermittent density lipoproteins (IDL), and low density
lipoproteins (LDL). ApoB functions as a recognition signal for the
cellular binding and internalization of LDL particles by the ApoB/E
receptor. An accumulation or overabundance of apolipoprotein
B-containing lipoproteins can lead to lipid-related disorders such
as atherosclerosis.
[0006] The development of therapies that reduce ApoB can be useful
for treating lipid-related disorders. One oligonucleotide based
therapy, in the form of antisense therapy, has been shown to reduce
ApoB levels in mouse in vivo, and treatments subsequently reduced
serum cholesterol and triglyceride levels (U.S. Publication No.
2003/0215943). These results demonstrated a moderate downregulation
of ApoB and its use as a target in treating lipid-related
disorders. The present invention advances the art by providing IRNA
agents that have been shown to reduce serum ApoB levels in
vivo.
SUMMARY
[0007] The invention provides compositions and methods for reducing
apolipoprotein B (ApoB) levels in a subject, e.g., a mammal, such
as a human. The method includes administering to a subject an iRNA
agent that silences an ApoB gene. The iRNA agent can be one
described here, or can be a dsRNA that is based on one of the
active sequences and target an identical region of the ApoB gene,
e.g., a mammalian ApoB gene, such as an ApoB gene from a human or
mouse. The iRNA agent can comprise less than 30 nucleotides per
strand, e.g., 21-23 nucleotides and consist of, comprise or be
derived from one of the agents provided herein under agent numbers
1-74. These preferred iRNA agents include four or more nucleotide
mismatches to all non-ApoB gene sequences in the subject.
[0008] The invention specifically provides an iRNA agent that
includes a sense strand having at least 15 contiguous nucleotides
of the sense strand sequences, and an antisense strand having at
least 15 contiguous nucleotides of the antisense sequences, of the
iRNA agents provided herein under agent numbers 1-74, e.g. agent
number 1, sense strand sequence 5'-cuuuacaagccuugguucagu-3' (SEQ.
ID NO. 153), antisense strand sequence
5'-acugaaccaaggcuuguaaagug-3'(SEQ. ID No. 154).
[0009] It shall be understood that, while some of the iRNA agents
provided herein encompass specific preferred patterns of modified
nucleotides, e.g. agent numbers 54 to 74, the iRNA agents of agent
numbers 1-53 are provided as blueprints. They are meant to
encompass such modifications as are evident to the skilled person
as equivalent to the iRNA agents of agent numbers 1-53, such as are
further described below, e.g. 2'-O-methyl modifications, generic
base substitutions, etc, that the skilled person would not expect
to alter the properties of these agents, and specifically the
ability of the two strands to hybridize under stringent conditions
with their complementary counterparts.
TABLE-US-00001 TABLE 1 Exemplary iRNA agents to target ApoB SEQ.
SEQ. ID ID Duplex Agent No. Sequence sense strand.sup.a No.
Sequence antisense strand.sup.a descriptora number 153
uuuacaagccuugguucagu 154 cugaaccaaggcuuguaaagug AL-DUP 5097 1 155
gaaucuuauauuugauccaa 156 uggaucaaauauaagauucccu AL-DUP 5098 2 161
agaagggaaucuuauauuug 162 aaauauaagauucccuucuauu AL-DUP 5101 3 147
ccccaucacuuuacaagccu 148 ggcuuguaaagugauggggcug AL-DUP 5094 4 159
aauagaagggaaucuuauau 160 uauaagauucccuucuauuuug AL-DUP 5100 5 145
cacauccuccaguggcugaa 146 ucagccacuggaggaugugagu AL-DUP 5093 6 49
gguguauggcuucaacccug 50 aggguugaagccauacaccucu AL-DUP 5024 7 127
ugaacaucaagaggggcauc 128 augccccucuugauguucagga AL-DUP 5084 8 137
aguuugugacaaauaugggc 138 cccauauuugucacaaacucca AL-DUP 5089 9 93
ucaagugucaucacacugaa 94 ucagugugaugacacuugauuu AL-DUP 5046 10 97
ucaucacacugaauaccaau 98 uugguauucagugugaugacac AL-DUP 5048 11 95
caagugucaucacacugaau 96 uucagugugaugacacuugauu AL-DUP 5047 12 99
uguccauucaaaacuaccac 100 ugguaguuuugaauggacaggu AL-DUP 5049 13 129
gaacaucaagaggggcauca 130 gaugccccucuugauguucagg AL-DUP 5085 14 135
gccccaucacuuuacaagcc 136 gcuuguaaagugauggggcugg AL-DUP 5088 15 131
uccagccccaucacuuuaca 132 guaaagugauggggcuggacac AL-DUP 5086 16 27
guguauggcuucaacccuga 28 caggguugaagccauacaccuc AL-DUP 5013 17 107
accuguccauucaaaacuac 108 uaguuuugaauggacaggucaa AL-DUP 5053 18 143
uugggaagaagaggcagcuu 144 agcugccucuucuucccaauua AL-DUP 5092 19 123
aacacuaagaaccagaagau 124 ucuucugguucuuaguguuagc AL-DUP 5061 20 57
agguguauggcuucaacccu 58 ggguugaagccauacaccucuu AL-DUP 5028 21 41
uguauggcuucaacccugag 42 ucaggguugaagccauacaccu AL-DUP 5020 22 157
aagggaaucuuauauuugau 158 ucaaauauaagauucccuucua AL-DUP 5099 23 59
ggcuucaacccugagggcaa 60 ugcccucaggguugaagccaua AL-DUP 5029 24 63
uauggcuucaacccugaggg 64 ccucaggguugaagccauacac AL-DUP 5031 25 121
aagugucaucacacugaaua 122 auucagugugaugacacuugau AL-DUP 5060 26 55
aaaucaagugucaucacacu 56 gugugaugacacuugauuuaaa AL-DUP 5027 27 39
ugacaaauaugggcaucauc 40 augaugcccauauuugucacaa AL-DUP 5019 28 71
accaacuucuuccacgaguc 72 acucguggaagaaguugguguu AL-DUP 5035 29 73
augaacaccaacuucuucca 74 ggaagaaguugguguucaucug AL-DUP 5036 30 105
ccuguccauucaaaacuacc 106 guaguuuugaauggacagguca AL-DUP 5052 31 61
aacaccaacuucuuccacga 62 cguggaagaaguugguguucau AL-DUP 5030 32 45
auaccguguauggaaacugc 46 caguuuccauacacgguaucca AL-DUP 5022 33 133
agccccaucacuuuacaagc 134 cuuguaaagugauggggcugga AL-DUP 5087 34 5
auugauugaccuguccauuc 6 aauggacaggucaaucaaucuu AL-DUP 5002 35 77
gaugaacaccaacuucuucc 78 gaagaaguugguguucaucugg AL-DUP 5038 36 1
agccuugguucaguguggac 2 uccacacugaaccaaggcuuga AL-DUP 5000 37 117
caucacacugaauaccaaug 118 auugguauucagugugaugaca AL-DUP 5058 38 3
gaacaccaacuucuuccacg 4 guggaagaaguugguguucauc AL-DUP 5001 39 69
caccaacuucuuccacgagu 70 cucguggaagaaguugguguuc AL-DUP 5034 40 25
gauugaccuguccauucaaa 26 uugaauggacaggucaaucaau AL-DUP 5012 41 21
aaauggacucaucugcuaca 22 guagcagaugaguccauuugga AL-DUP 5010 42 29
cugugggauuccaucugcca 30 ggcagauggaaucccacagacu AL-DUP 5014 43 109
aucacacugaauaccaaugc 110 cauugguauucagugugaugac AL-DUP 5054 44 23
auugaccuguccauucaaaa 24 uuugaauggacaggucaaucaa AL-DUP 5011 45 33
caauuugaucaguauauuaa 34 uaauauacugaucaaauuguau AL-DUP 5016 46 83
caagccuugguucagugugg 84 cacacugaaccaaggcuuguaa AL-DUP 5041 47 79
uuccaucugccaucucgaga 80 cucgagauggcagauggaaucc AL-DUP 5039 48 43
accguguauggaaacugcuc 44 agcaguuuccauacacgguauc AL-DUP 5021 49 35
gacucaucugcuacagcuua 36 aagcuguagcagaugaguccau AL-DUP 5017 50 51
uuugugacaaauaugggcau 52 ugcccauauuugucacaaacuc AL-DUP 5025 51 65
uggcuucaacccugagggca 66 gcccucaggguugaagccauac AL-DUP 5032 52 125
aauuugaucaguauauuaaa 126 uuaauauacugaucaaauugua AL-DUP 5062 53
.sup.aSee Table 2 for an explanation of nucleotide representation
(e.g., lower case letters, bold and italicized letters).
[0010] As shown in Example 3 hereinbelow, the iRNA agents of Table
1, agent numbers 1-53, possess the advantageous and surprising
ability to reduce the amount of ApoB mRNA present in cultured human
HepG2 cells after incubation with these iRNA agents by more than
50% compared to cells which have not been incubated with the iRNA
agent, and/or to reduce the amount of ApoB protein secreted into
cell culture supernatant by cultured human HepG2 cells by more than
50% (see Table 8).
[0011] The invention further provides an iRNA agent that includes a
sense strand having at least 15 contiguous nucleotides of the sense
sequences of the iRNA agents, agent numbers 1-19, 24-26, 29, 30 and
32-42, and an antisense strand having at least 15 contiguous
nucleotides of the antisense sequences of the iRNA agents, agent
numbers 1-19, 24-26, 29, 30 and 32-42. As shown in Example 3
hereinbelow, the iRNA agents, agent numbers 1-19, 24-26, 29, 30 and
32-42, possess the advantageous and surprising ability to reduce
the amount of ApoB mRNA present in cultured human HepG2 cells after
incubation with these iRNA agents by more than 60% compared to
cells which have not been incubated with the iRNA agent, and/or to
reduce the amount of ApoB protein secreted into cell culture
supernatant by more than 60% (see Table 8).
[0012] The invention further provides an iRNA agent that includes a
sense strand having at least 15 contiguous nucleotides of the sense
sequences of the agents provided in Table 1, agent numbers 1-12,
15, 17, 24, 29, 30 and 32-35, and an antisense strand having at
least 15 contiguous nucleotides of the antisense sequences of the
agents provided in Table 1, agent numbers 1-12, 15, 17, 24, 29, 30
and 32-35. As shown in Example 3 hereinbelow, these iRNA agents
possess the advantageous and surprising ability to reduce the
amount of ApoB mRNA present in cultured human HepG2 cells after
incubation with these agents by more than 70% compared to cells
which have not been incubated with the agent, and/or to reduce the
amount of ApoB protein secreted into cell culture supernatant by
more than 70% (see Table 8).
[0013] The invention further provides an iRNA agent that includes a
sense strand having at least 15 contiguous nucleotides of the sense
sequences of the iRNA agents, agent numbers 1-5, 7, and 11, and an
antisense strand having at least 15 contiguous nucleotides of the
antisense sequences of the iRNA agents, agent numbers 1-5, 7, and
11. As shown in Example 3 hereinbelow, these iRNA agents possess
the advantageous and surprising ability to reduce the amount of
ApoB mRNA present in cultured human HepG2 cells after incubation
with these agents by more than 80% compared to cells which have not
been incubated with the agent, and/or to reduce the amount of ApoB
protein secreted into cell culture supernatant by more than 80%
(see Table 8).
[0014] In a particularly preferred aspect, the iRNA agent is
selected from the group of: the iRNA agent, agent number 54, 55,
56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72,
73, or 74.
[0015] In another preferred embodiment, the iRNA agent reduces the
amount of ApoB mRNA present in cultured human HepG2 cells after
incubation with the iRNA agent by more than 50% compared to cells
which have not been incubated with the agent, and/or reduces the
amount of ApoB protein secreted into cell culture supernatant by
cultured human HepG2 cells by more than 50%, and/or reduces the
amount of apo-B mRNA present in murine liver cells of C57Bl/6 mice
by at least 20% in vivo after administration of 50 mg/kg body
weight or 100 mg/kg body weight.
[0016] Further provided by the instant invention are iRNA agents
comprising a sense strand and antisense strand each comprising a
sequence of at least 16, 17 or 18 nucleotides which is essentially
identical, as defined below, to one of the sequences of the iRNA
agents, agent numbers 1-74, except that not more than 1, 2 or 3
nucleotides per strand, respectively, have been substituted by
other nucleotides (e.g. adenosine replaced by uracil), while
essentially retaining the ability to inhibit ApoB expression in
cultured human HepG2 cells, as defined below.
[0017] In one embodiment, the iRNA agent is at least 15 nucleotides
long and includes a sense RNA strand and an antisense RNA strand,
wherein the antisense RNA strand is 30 or fewer nucleotides in
length, and the duplex region of the iRNA agent is 15-30,
preferably 18-25 nucleotide pairs in length. The iRNA agent may
further include a nucleotide overhang having 1 to 4, preferably 2
to 3, unpaired nucleotides, and the unpaired nucleotides may have
at least one phosphorothioate dinucleotide linkage. The nucleotide
overhang can be, e.g., at the 3'-end of the antisense strand of the
iRNA agent.
[0018] In one embodiment, the iRNA agent inhibits the expression of
human and mouse ApoB, e.g. in human HepG2 and mouse NmuLi
cells.
[0019] In one embodiment, and as described herein, it is preferred
that the IRNA agent be modified by attachment of a hydrophobic
moiety, e.g. a cholesterol-comprising moiety, preferably to the
sense strand of the iRNA agent, and more preferably to the 3'-end
of the sense strand of the iRNA agent.
[0020] In another embodiment, and as described herein, it is
preferred that the iRNA agent be modified to improve stability.
Preferred modifications are the introduction of phosphorothioate
linkages and 2'-substitutions on the ribose unit, e.g., 2'-deoxy,
2'-deoxy-2'-fluoro, 2'-O-methyl, 2'-O-methoxyethyl (2'-O-MOE),
2'-O-aminopropyl (2'-O-AP), 2'-O-dimethylaminoethyl (2'-O-DMAOE),
2'-O-dimethylaminopropyl (2'-O-DMAP),
2'-O-dimethylaminoethyloxyethyl (2'-O-DMAEOE), or
2'-O--N-methylacetamido (2'-O-NMA) substitutions.
[0021] Preferably, these 2'-substitutions are made to the 5'
nucleotide of a 5'-UA-3' dinucleotide, a 5'-UG-3' dinucleotide, a
5'-CA-3' dinucleotide, a 5'-UU-3' dinucleotide, or a 5'-CC-3'
dinucleotide on the sense strand and, optionally, also on the
antisense strand of the iRNA agent, or to all pyrimidine-base
comprising nucleotides. More, preferably, the 5'-most pyrimidines
in all occurrences of the sequence motifs 5'-UA-3', 5'-CA-3',
5'-UU-3', and 5'-UG-3' are 2'-modified nucleotides. Yet more
preferably, all pyrimidines in the sense strand are 2'-modified
nucleotides, and the 5'-most pyrimidines in all occurrences of the
sequence motifs 5'-UA-3' and 5'-CA-3'. Most preferably, all
pyrimidines in the sense strand are 2'-modified nucleotides, and
the 5'-most pyrimidines in all occurrences of the sequence motifs
5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' are 2'-modified
nucleotides in the antisense strand.
[0022] In another embodiment, and as described herein, a
cholesterol moiety (e.g., on the 3'-end of the sense strand), a
2'-modification (e.g., a 2'-O-methyl or
2'-deoxy-2'-fluoro-modification), and a phosphorothioate (e.g., on
the 3'-most one or two nucleotides of the sense and antisense
strands) are present in the same iRNA agent.
[0023] In a preferred embodiment, administration of an iRNA agent,
e.g., an iRNA agent described herein, is for treatment of a disease
or disorder present in the subject in which ApoB expression plays a
role. In another preferred embodiment, administration of the iRNA
agent is for prophylactic treatment of ApoB mediated disorders.
[0024] In one aspect, the invention features preparations,
including substantially pure or pharmaceutically acceptable
preparations of iRNA agents which modulate e.g., inhibit, ApoB. The
preparations can include an iRNA agent that targets an ApoB
encoding nucleic acid and a pharmaceutically acceptable carrier. In
one embodiment, the iRNA agent has a sense strand having at least
15 contiguous nucleotides of the sense sequences of the iRNA
agents, agent numbers 1-74, and an antisense strand having at least
15 contiguous nucleotides of the antisense sequences of the iRNA
agents, agent numbers 1-74.
[0025] In another aspect, the invention features a method of
preparing a pharmaceutical composition, comprising formulating an
iRNA agent a sense strand having at least 15 contiguous nucleotides
of the sense sequences of the iRNA agents, agent numbers 1-74, and
an antisense strand having at least 15 contiguous nucleotides of
the antisense sequences of the iRNA agents, agent numbers 1-74,
with a pharmaceutically acceptable carrier.
[0026] The pharmaceutical composition of the invention can be
administered in an amount sufficient to reduce expression of ApoB
messenger RNA (mRNA). In one embodiment, the iRNA agent is
administered in an amount sufficient to reduce expression of ApoB
protein (e.g., by at least 2%, 4%, 6%, 10%, 15%, 20% or
greater).
[0027] The pharmaceutical composition of the invention can be
administered to a subject, wherein the subject is at risk for or
suffering from a disorder characterized by elevated or otherwise
unwanted expression of ApoB, elevated or otherwise unwanted levels
of cholesterol, a lipid-mediated vascular disorder, and/or
disregulation of lipid metabolism. The iRNA agent can be
administered to an individual diagnosed with or having the
disorder, or at risk for the disorder to delay onset of the
disorder or a symptom of the disorder. These disorders include
HDL/LDL cholesterol imbalance; dyslipidemias, e.g., familial
combined hyperlipidemia (FCHL), acquired hyperlipidemia;
hypercholestorolemia; statin-resistant hypercholesterolemia;
coronary artery disease (CAD); coronary heart disease (CHD);
thrombosis; and atherosclerosis. In one embodiment, the iRNA that
targets ApoB is administered to a subject suffering from
statin-resistant hypercholesterolemia.
[0028] The pharmaceutical composition of the invention can be
administered in an amount sufficient to reduce levels of serum LDL
cholesterol and/or HDL cholesterol and/or total cholesterol in a
subject. For example, the iRNA is administered in an amount
sufficient to decrease total cholesterol by at least 0.5%, 1%,
2.5%, 5%, 10% or more in the subject. In one embodiment, the
pharmaceutical composition of the invention is administered in an
amount sufficient to reduce the risk of myocardial infarction in
the subject. In a preferred embodiment the pharmaceutical
composition is administered repeatedly.
[0029] In one embodiment, the iRNA agent can be targeted to the
liver, and ApoB expression levels are decreased in the liver
following administration of the ApoB iRNA agent. For example, the
iRNA agent can be complexed with a moiety that targets the liver,
e.g., an antibody or ligand, such as cholesterol that binds a
receptor on liver cells. As shown in Example 7G) below, the
conjugation of a cholesterol-comprising moiety led to efficient
uptake of siRNAs by liver tissue and decreased ApoB mRNA levels in
liver samples. This shows that modifications such as a conjugation
with a cholesterol-comprising moiety allows for the use of iRNA
agents in vivo to target genes in the liver.
[0030] In one embodiment, the iRNA agent can be targeted to the
gut, e.g., to the intestine, such as to the jejunum of the
intestine, and ApoB expression levels are decreased in the gut
following administration of the ApoB iRNA agent. Unexpectedly, it
was found that an iRNA agent conjugated to a cholesterol moiety can
be used to target an IRNA agent to the gut. As shown in Example 7G)
below, the conjugation of a cholesterol-comprising moiety led to
efficient uptake of siRNAs by intestinal tissues and decreased ApoB
mRNA levels in intestinal tissue samples. This shows that
modifications such as a conjugation with a cholesterol-comprising
moiety allows for the use of iRNA agents in vivo to target genes in
tissues of the gut.
[0031] In one embodiment, the iRNA agent has been modified, or is
associated with a delivery agent, e.g., a delivery agent described
herein, e.g., a liposome. In one embodiment, the modification
mediates association with a serum albumin (SA), e.g., a human serum
albumin (HSA), or a fragment thereof.
[0032] A method of evaluating an iRNA agent thought to inhibit the
expression of an ApoB-gene, the method comprising: [0033] a.
providing an iRNA agent, wherein a first strand is sufficiently
complementary to a nucleotide sequence of an ApoB mRNA, and a
second strand is sufficiently complementary to the first strand to
hybridize to the first strand; [0034] b. contacting the iRNA agent
to a cell comprising an ApoB gene; [0035] c. comparing ApoB gene
expression before contacting the iRNA agent to the cell, or of
uncontacted control cells, to the ApoB gene expression after
contacting the iRNA agent to the cell; and [0036] d. determining
whether the iRNA agent is useful for inhibiting ApoB gene
expression, wherein the iRNA is useful if the amount of ApoB RNA
present in the cell, or protein secreted by the cell, is less than
the amount prior to contacting the iRNA agent to the cell.
[0037] In one embodiment, steps b.-d. are performed both in vitro
and in non-human laboratory animals in vivo. In another embodiment.
The method further comprises determining the activity of the iRNA
agent in activating interferon-.alpha. production by peripheral
blood mononuclear cells.
[0038] The methods and compositions of the invention, e.g., the
methods and compositions to treat diseases and disorders of the
liver described herein, can be used with any of the iRNA agents
described. In addition, the methods and compositions of the
invention can be used for the treatment of any disease or disorder
described herein, and for the treatment of any subject, e.g., any
animal, any mammal, such as any human.
[0039] The methods and compositions of the invention, e.g., the
methods and iRNA compositions to treat lipid metabolism disorders
described herein, can be used with any dosage and/or formulation
described herein, as well as with any route of administration
described herein.
[0040] The details of one or more embodiments of the invention are
set forth in the accompanying drawings and the description below.
Other features, objects, and advantages of the invention will be
apparent from this description, the drawings, and from the claims.
This application incorporates all cited references, patents, and
patent applications by references in their entirety for all
purposes.
BRIEF DESCRIPTION OF DRAWINGS
[0041] FIG. 1 is a schematic illustrating the synthesis and
structure of cholesterol conjugated RNA strands. The sphere
represents the solid phase (controlled pore glass, CPG).
[0042] FIG. 2 is a graph depicting the ratio [ApoB mRNA]/[GAPDH
control mRNA] following treatment of cells with increasing levels
of siRNA, AL-DUP5024. Determination of the inhibitor concentration
at 50% maximal inhibition (IC.sub.50) was determined by curve
fitting using the computer software Xlfit using the following
parameters: Dose Response One Site, 4 Parameter Logistic Model,
fit=(A+((B-A)/(1+(((10 C)/x) D)))), inv=((10 C)/((((B-A)/(y-A))-1)
(1/D))), res=(y-fit).
[0043] FIG. 3 is a panel of polyacrylamide gels depicting the
degradation of siRNA duplexes AL-DUP 5024, AL-DUP 5163, AL-DUP
5164, AL-DUP 5165, AL-DUP 5166, AL-DUP 5180, and AL-DUP 5181 by
mouse serum nucleases. siRNA duplexes were incubated in mouse serum
for 0, 1, 3, 6 or 24 hours. The lanes marked "unb" represent an
untreated control.
[0044] FIG. 4 is a panel of polyacrylamide gels depicting the
degradation of siRNA duplexes AL-DUP 5167, AL-DUP 5168, AL-DUP
5048, AL-DUP 5169, AL-DUP 5170, AL-DUP 5182, and AL-DUP 5183 by
mouse serum nucleases. siRNA duplexes were incubated in mouse serum
for 0, 1, 3, 6 or 24 hours. The lanes marked "unb" represent an
untreated control.
[0045] FIG. 5A is a dose-response plot of ApoB protein secretion
into supernatant by cultured human HepG2 cells incubated with media
containing 100, 33, 11, 3.7, 1.2, 0.4, 0.14, or 0.05 nM of
ApoB-specific siRNA duplex AL-DUP 5163. The response is expressed
as the ratio of ApoB protein concentrations in the supernatant of
cells treated with the ApoB-specific siRNA duplex to the ApoB
concentration in the supernatant of cells treated with an
unspecific control siRNA duplex with (AL-DUP 5129, diamonds) or
without (AL-DUP HCV, squares) cholesterol-conjugation.
[0046] FIG. 5B is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5164 at the concentration ranges
described for FIG. 5A.
[0047] FIG. 5C is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5165 at the concentration ranges
described for FIG. 5A.
[0048] FIG. 5D is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5166 at the concentration ranges
described for FIG. 5A.
[0049] FIG. 5E is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5180 at the concentration ranges
described for FIG. 5A.
[0050] FIG. 5F is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5181 at the concentration ranges
described for FIG. 5A.
[0051] FIG. 5G is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5167 at the concentration ranges
described for FIG. 5A.
[0052] FIG. 5H is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5168 at the concentration ranges
described for FIG. 5A.
[0053] FIG. 5I is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5169 at the concentration ranges
described for FIG. 5A.
[0054] FIG. 5J is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5170 at the concentration ranges
described for FIG. 5A.
[0055] FIG. 5K is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5182 at the concentration ranges
described for FIG. 5A.
[0056] FIG. 5L is a dose-response plot of ApoB protein secretion
according to the method described in FIG. 5A. The HepG2 cells were
incubated with the siRNA duplex 5183 at the concentration ranges
described for FIG. 5A.
[0057] FIG. 6A to D depict, by way of example, results obtained in
experiments described in Example 7, (H), below.
[0058] FIG. 6A is an S1-nuclease protection assay with radiolabeled
probes complementary to antisense strands of siRNAs. The assay was
used to detect siRNAs in pooled liver and jejunum tissue lysates
from animals injected with saline ("-"), AL-DUP 5386 ("A"), AL-DUP
5311 ("B"), AL-DUP 5385 ("C2"), and AL-DUP 5167 ("C1"). The three
cholesterol-conjugated siRNAs were detected at comparable levels in
liver and jejunum, but the non-cholesterol-conjugated siRNA AL-DUP
5385 remained below detection levels in both tissues. S1-nuclease
protection assay for endogeneous miRNAs served as a loading
controls for jejunum (miRNA 143, sequence
5'-UGAGAUGAAGCACUGUAGCUCA-3', SEQ. ID NO. 270) and liver (miRNA
122, sequence 5'-UGGAGUGUGACAAUGGUGUUUG-3', SEQ. ID NO. 269).
[0059] FIG. 6B is a graph depicting the results of branched-DNA
assays to detect ApoB mRNA levels in mouse liver and jejunum tissue
following siRNA treatment. Tissue lysates were used for ApoB and
GAPDH mRNA quantification and the ratio of ApoB and GAPDH mRNA was
calculated and expressed as a group average relative to a saline
control group. Bars represent group mean values. Error bars
represent the standard deviation of the mean. Asterisks above bars
in bar graphs denote groups significantly different compared to
saline control animals at p<0.01.
[0060] FIG. 6C is a graph depicting the results of ELISA assays to
measure plasma ApoB protein levels following siRNA treatment.
ApoB-100 from plasma samples of individual animals was detected
using the primary antibody LF3 against mouse ApoB-100. Mean group
values of ApoB protein level are represented relative to the mean
of saline control. Bars represent group mean values. Error bars
represent the standard deviation of the mean. Asterisks above bars
in bar graphs denote groups significantly different compared to
saline control animals p<0.01.
[0061] FIG. 6D is a graph depicting total plasma ApoB protein
levels following siRNA treatment. Total plasma cholesterol levels
where measured using the Cholesterol detection kit (Diasys). Bars
represent group mean values. Error bars represent the standard
deviation of the mean. Asterisks above bars in bar graphs denote
groups significantly different compared to saline control animals
p<0.01.
[0062] FIG. 7A is a schematic representation of the ApoB mRNA and
of the adapter ligated ApoB cDNA used for 5'-RACE PCR. The
schematic shows the relative target sites of the AL-DUP 5167 siRNA
and the PCR primers, and the size of PCR reaction products.
[0063] FIG. 7B is an agarose gel of RACE-PCR amplification 3. The
electrophoretic analysis indicates specific cleavage products in
liver and jejunum of mice treated with ApoB specific AL-DUP 5167
only. The lanes of the gel are marked by capital letters that
indicate treatment groups and controls. The lanes are marked as
follows: A: PBS; B: AL-DUP 5386; C: AL-DUP 5167; D: AL-DUP 5163, E:
AL DUP 5385; F: AL-DUP 5311; Fc: Control, Forward primer only using
cDNA from group C; RC: Control, Reverse primer only using cDNA from
group C.
DETAILED DESCRIPTION
[0064] For ease of exposition the term "nucleotide" or
"ribonucleotide" is sometimes used herein in reference to one or
more monomeric subunits of an RNA agent. It will be understood that
the usage of the term "ribonucleotide" or "nucleotide" herein can,
in the case of a modified RNA or nucleotide surrogate, also refer
to a modified nucleotide, or surrogate replacement moiety, as
further described below, at one or more positions.
[0065] An "RNA agent" as used herein, is an unmodified RNA,
modified RNA, or nucleoside surrogate, all of which are described
herein. While numerous modified RNAs and nucleoside surrogates are
described, preferred examples include those which have greater
resistance to nuclease degradation than do unmodified RNAs.
Preferred examples include those that have a 2' sugar modification,
a modification in a single strand overhang, preferably a 3' single
strand overhang, or, particularly if single stranded, a
5'-modification which includes one or more phosphate groups or one
or more analogs of a phosphate group.
[0066] An "iRNA agent" (abbreviation for "interfering RNA agent")
as used herein, is an RNA agent, which can downregulate the
expression of a target gene, e.g., ApoB. While not wishing to be
bound by theory, an iRNA agent may act by one or more of a number
of mechanisms, including post-transcriptional cleavage of a target
mRNA sometimes referred to in the art as RNAi, or
pre-transcriptional or pre-translational mechanisms. An iRNA agent
can include a single strand or can include more than one strands,
e.g., it can be a double stranded (ds) iRNA agent. If the iRNA
agent is a single strand it is particularly preferred that it
include a 5' modification which includes one or more phosphate
groups or one or more analogs of a phosphate group.
[0067] A "single strand iRNA agent" as used herein, is an iRNA
agent which is made up of a single molecule. It may include a
duplexed region, formed by intra-strand pairing, e.g., it may be,
or include, a hairpin or panhandle structure. Single strand iRNA
agents are preferably antisense with regard to the target
molecule.
[0068] A "ds iRNA agent" (abbreviation for "double stranded iRNA
agent"). as used herein, is an iRNA agent which includes more than
one, and preferably two, strands in which interchain hybridization
can form a region of duplex structure.
[0069] Although, in mammalian cells, long ds iRNA agents can induce
the interferon response which is frequently deleterious, short ds
iRNA agents do not trigger the interferon response, at least not to
an extent that is deleterious to the cell and host. The iRNA agents
of the present invention include molecules which are sufficiently
short that they do not trigger the interferon response in mammalian
cells. Thus, the administration of a composition of an iRNA agent
(e.g., formulated as described herein) to a mammalian cell can be
used to silence expression of the ApoB gene while circumventing the
interferon response. Molecules that are short enough that they do
not trigger an interferon response are termed siRNA agents or
siRNAs herein. "siRNA agent" or "siRNA" as used herein, refers to
an iRNA agent, e.g., a ds iRNA agent or single strand RNA agent,
that is sufficiently short that it does not induce a deleterious
interferon response in a human cell, e.g., it has a duplexed region
of less than 60 but preferably less than 50, 40, or 30 nucleotide
pairs.
[0070] Moreover, in one embodiment, a mammalian cell is treated
with an iRNA agent that disrupts a component of the interferon
response, e.g., dsRNA-activated protein kinase PKR.
[0071] The isolated iRNA agents described herein, including ds iRNA
agents and siRNA agents, can mediate silencing of an ApoB gene,
e.g., by RNA degradation. For convenience, such RNA is also
referred to herein as the RNA to be silenced. Such a gene is also
referred to as a target gene. Preferably, the RNA to be silenced is
a gene product of an endogenous ApoB gene.
[0072] As used herein, the phrase "mediates RNAi" refers to the
ability of an agent to silence, in a sequence specific manner, a
target gene. "Silencing a target gene" means the process whereby a
cell containing and/or secreting a certain product of the target
gene when not in contact with the agent, will contain and/or secret
at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% less of
such gene product when contacted with the agent, as compared to a
similar cell which has not been contacted with the agent. Such
product of the target gene can, for example, be a messenger RNA
(mRNA), a protein, or a regulatory element. While not wishing to be
bound by theory, it is believed that silencing by the agents
described herein uses the RNAi machinery or process and a guide
RNA, e.g., an siRNA agent of 15 to 30 nucleotide pairs.
[0073] As used herein, "the term "complementary" is used to
indicate a sufficient degree of complementarity such that stable
and specific binding occurs between a compound of the invention and
a target RNA molecule, e.g. an ApoB mRNA molecule. Specific binding
requires a sufficient degree of complementarity to avoid
non-specific binding of the oligomeric compound to non-target
sequences under conditions in which specific binding is desired,
i.e., under physiological conditions in the case of in vivo assays
or therapeutic treatment, or in the case of in vitro assays, under
conditions in which the assays are performed. The non-target
sequences typically differ by at least 4 nucleotides.
[0074] As used herein, an iRNA agent is "sufficiently
complementary" to a target RNA, e.g., a target mRNA (e.g., a target
ApoB mRNA) if the iRNA agent reduces the production of a protein
encoded by the target RNA in a cell. The iRNA agent may also be
"exactly complementary" (excluding the SRMS containing subunit(s))
to the target RNA, e.g., the target RNA and the iRNA agent anneal,
preferably to form a hybrid made exclusively of Watson-Crick
basepairs in the region of exact complementarity. A "sufficiently
complementary" iRNA agent can include an internal region (e.g., of
at least 10 nucleotides) that is exactly complementary to a target
ApoB RNA. Moreover, in some embodiments, the iRNA agent
specifically discriminates a single-nucleotide difference. In this
case, the iRNA agent only mediates RNAi if exact complementary is
found in the region (e.g., within 7 nucleotides of) the
single-nucleotide difference. Preferred iRNA agents will be based
on or consist or comprise the sense and antisense sequences
provided in Table 1.
[0075] As used herein, "essentially identical" when used referring
to a first nucleotide sequence in comparison to a second nucleotide
sequence means that the first nucleotide sequence is identical to
the second nucleotide sequence except for up to one, two or three
nucleotide substitutions (e.g. adenosine replaced by uracil).
"Essentially retaining the ability to inhibit ApoB expression in
cultured human HepG2 cells", as used herein referring to an iRNA
agent not identical to but derived from one of the iRNA agents of
Table 1 by deletion, addition or substitution of nucleotides, means
that the derived iRNA agent possesses an inhibitory activity lower
by not more than 20% inhibition compared to the iRNA agent of Table
1 it was derived from. E.g. an iRNA agent derived from an iRNA
agent of Table 1 which lowers the amount of ApoB mRNA present in
cultured human HepG2 cells by 70% may itself lower the amount of
ApoB mRNA present in cultured human HepG2 cells by at least 50% in
order to be considered as essentially retaining the ability to
inhibit ApoB expression in cultured human HepG2 cells. Optionally,
an iRNA agent of the invention may lower the amount of ApoB mRNA
present in cultured human HepG2 cells, or the amount of ApoB
protein secreted into cell culture supernatant, by at least
50%.
[0076] In a typical embodiment, the subject is a mammal such as a
cow, horse, mouse, rat, dog, pig, goat, or a primate. In a much
preferred embodiment, the subject is a human, e.g., a normal
individual or an individual that has, is diagnosed with, or is
predicted to have a disease or disorder.
[0077] Because iRNA agent mediated silencing can persist for
several days after administering the iRNA agent composition, in
many instances, it is possible to administer the composition with a
frequency of less than once per day, or, for some instances, only
once for the entire therapeutic regimen.
[0078] Disorders Associated with ApoB Misexpression
[0079] An iRNA agent that targets ApoB, e.g., an iRNA agent
described herein, can be used to treat a subject, e.g., a human
having or at risk for developing a disease or disorder associated
with aberrant or unwanted ApoB gene expression, e.g., ApoB
overexpression.
[0080] For example, an iRNA agent that targets ApoB mRNA can be
used to treat a lipid-related disorder, such as
hypercholesterolemia, e.g., primary hypercholesterolemia with
peripheral vascular disease. Other lipid-related disorders include
coronary artery disease (CAD), myocardial infarction; HDL/LDL
cholesterol imbalance; dyslipidemias (e.g., familial combined
hyperlipidemia (FCHL) and acquired hyperlipidemia);
hypercholestorolemia; statin-resistant hypercholesterolemia;
coronary heart disease (CHD); thrombosis; and atherosclerosis. In
one embodiment, the iRNA that targets ApoB mRNA is administered to
a subject suffering from statin-resistant disorder, e.g.
statin-resistant hypercholesterolemia. The subject can be one who
is currently being treated with a statin, one who has been treated
with a statin in the past, or one who is unsuited for treatment
with a statin.
[0081] An iRNA agent targeting ApoB mRNA can be used to treat a
human carrying a genetic mutation or polymorphism in the ApoB gene
or in the LDL-receptor. For example, the iRNA agent can be used to
treat a human diagnosed as having familial ligand-defective
apolipoprotein B-100 (FDB), a dominantly inherited disorder of
lipoprotein metabolism leading to hypercholesterolemia and
increased proneness to CAD. Plasma cholesterol levels are
dramatically elevated in these subjects due to impaired clearance
of LDL particles by defective ApoB/E receptors.
[0082] Design and Selection of iRNA Agents
[0083] Example 2 hereinbelow shows a gene walk based on sequence
prediction was used to evaluate 81 potential iRNA agents targeting
human and mouse ApoB mRNA. Based on the results provided, Table 1
provides active iRNA agents targeting ApoB. One can readily design
and generate other iRNA agents that are based on, comprise or
consist of one of the active sequences provided herein such that at
least a portion of an active sequence is included in the iRNA
agents.
[0084] The iRNA agents shown in Example 2 hereinbelow are composed
of a sense strand of 21 nucleotides in length, and an antisense
strand of 23 nucleotides in length. However, while these lengths
may potentially be optimal, the iRNA agents are not meant to be
limited to these lengths. The skilled person is well aware that
shorter or longer iRNA agents may be similarly effective, since,
within certain length ranges, the efficacy is rather a function of
the nucleotide sequence than strand length. For example, Yang, D.,
et al., PNAS 2002, 99:9942-9947, demonstrated similar efficacies
for iRNA agents of lengths between 21 and 30 base pairs. Others
have shown effective silencing of genes by iRNA agents down to a
length of approx. 15 base pairs (Byrom, W. M., et al., Inducing
RNAi with siRNA Cocktails Generated by RNase III; Tech Notes 10(1),
Ambion, Inc., Austin, Tex., USA).
[0085] Therefore, it is possible and contemplated by the instant
invention to select from the sequences provided in Table 1 a
partial sequence of between 15 to 22 nucleotides for the generation
of an iRNA agent derived from one of the sequences provided in
Table 1. Alternatively, one may add one or several nucleotides to
one of the sequences provided in Table 1, preferably, but not
necessarily, in such a fashion that the added nucleotides are
complementary to the respective sequence of the target gene, e.g.
ApoB. All such derived iRNA agents are included in the iRNA agents
of the rpesent invention, provided they essentially retain the
ability to inhibit ApoB expression in cultured human HepG2
cells.
[0086] Generally, the iRNA agents of the instant invention include
a region of sufficient complementarity to the ApoB gene, and are of
sufficient length in terms of nucleotides, that the iRNA agent, or
a fragment thereof, can mediate down regulation of the ApoB gene.
The antisense strands of the iRNA agents of Table 1 are fully
complementary to the mRNA sequences of mouse (GenBank Accession
number: XM.sub.--137955) and human (GenBank Accession number:
NM.sub.--000384) ApoB, and their sense strands are fully
complementary to the antisense strands except for the two
3'-terminal nucleotides on the antisense strand. However, it is not
necessary that there be perfect complementarity between the iRNA
agent and the target, but the correspondence must be sufficient to
enable the iRNA agent, or a cleavage product thereof, to direct
sequence specific silencing, e.g., by RNAi cleavage of an ApoB
mRNA.
[0087] Therefore, the iRNA agents of the instant invention include
agents comprising a sense strand and antisense strand each
comprising a sequence of at least 16, 17 or 18 nucleotides which is
essentially identical, as defined below, to one of the sequences of
Table 1, except that not more than 1, 2 or 3 nucleotides per
strand, respectively, have been substituted by other nucleotides
(e.g. adenosine replaced by uracil), while essentially retaining
the ability to inhibit ApoB expression in cultured human HepG2
cells, as defined below. These agents will therefore possess at
least 15 nucleotides identical to one of the sequences of Table 1,
but 1, 2 or 3 base mismatches with respect to either the target
ApoB mRNA sequence or between the sense and antisense strand are
introduced. Mismatches to the target ApoB mRNA sequence,
particularly in the antisense strand, are most tolerated in the
terminal regions and if present are preferably in a terminal region
or regions, e.g., within 6, 5, 4, or 3 nucleotides of a 5' and/or
3' terminus, most preferably within 6, 5, 4, or 3 nucleotides of
the 5'-terminus of the sense strand or the 3'-terminus of the
antisense strand. The sense strand need only be sufficiently
complementary with the antisense strand to maintain the overall
double stranded character of the molecule.
[0088] The antisense strand of an iRNA agent should be equal to or
at least, 14, 15, 16 17, 18, 19, 25, 29, 40, or 50 nucleotides in
length. It should be equal to or less than 60, 50, 40, or 30,
nucleotides in length. Preferred ranges are 15-30, 17 to 25, 19 to
23, and 19 to 21 nucleotides in length.
[0089] The sense strand of an iRNA agent should be equal to or at
least 14, 15, 16 17, 18, 19, 25, 29, 40, or 50 nucleotides in
length. It should be equal to or less than 60, 50, 40, or 30
nucleotides in length. Preferred ranges are 15-30, 17 to 25, 19 to
23, and 19 to 21 nucleotides in length.
[0090] The double stranded portion of an iRNA agent should be equal
to or at least, 15, 16 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 40,
or 50 nucleotide pairs in length. It should be equal to or less
than 60, 50, 40, or 30 nucleotides pairs in length. Preferred
ranges are 15-30, 17 to 25, 19 to 23, and 19 to 21 nucleotides
pairs in length.
[0091] It is preferred that the sense and antisense strands be
chosen such that the iRNA agent includes a single strand or
unpaired region at one or both ends of the molecule. Thus, an iRNA
agent contains sense and antisense strands, preferably paired to
contain an overhang, e.g., one or two 5' or 3' overhangs but
preferably a 3' overhang of 2-3 nucleotides. Most embodiments will
have a 3' overhang. Preferred siRNA agents will have
single-stranded overhangs, preferably 3' overhangs, of 1 to 4, or
preferably 2 or 3 nucleotides, in length at each end. The overhangs
can be the result of one strand being longer than the other, or the
result of two strands of the same length being staggered. 5'-ends
are preferably phosphorylated.
[0092] Preferred lengths for the duplexed region is between 15 and
30, most preferably 18, 19, 20, 21, 22, and 23 nucleotides in
length, e.g., in the siRNA agent range discussed above. siRNA
agents can resemble in length and structure the natural Dicer
processed products from long dsRNAs. Embodiments in which the two
strands of the siRNA agent are linked, e.g., covalently linked are
also included. Hairpin, or other single strand structures which
provide the required double stranded region, and preferably a 3'
overhang are also within the invention.
[0093] Much of the discussion below refers to single strand
molecules. In many embodiments of the invention a ds iRNA agent,
e.g., a partially ds iRNA agent, is required or preferred. Thus, it
is understood that that double stranded structures (e.g. where two
separate molecules are contacted to form the double stranded region
or where the double stranded region is formed by intramolecular
pairing (e.g., a hairpin structure)) made of the single stranded
structures described below are within the invention. Preferred
lengths are described elsewhere herein.
[0094] Evaluation of Candidate iRNA Agents
[0095] A candidate iRNA agent can be evaluated for its ability to
downregulate target gene expression. For example, a candidate iRNA
agent can be provided, and contacted with a cell, e.g. a HepG2
cell, that expresses the target gene, e.g., the ApoB gene, either
endogenously or because it has been transfected with a construct
from which ApoB can be expressed. The level of target gene
expression prior to and following contact with the candidate iRNA
agent can be compared, e.g. on an mRNA or protein level. If it is
determined that the amount of RNA or protein expressed from the
target gene is lower following contact with the iRNA agent, then it
can be concluded that the iRNA agent downregulates target gene
expression. The level of target ApoB RNA or ApoB protein in the
cell can be determined by any method desired. For example, the
level of target RNA can be determined by Northern blot analysis,
reverse transcription coupled with polymerase chain reaction
(RT-PCR), or RNAse protection assay. The level of protein can be
determined, for example, by Western blot analysis.
[0096] Stability Testing, Modification, and Retesting of iRNA
Agents
[0097] A candidate iRNA agent can be evaluated with respect to
stability, e.g, its susceptibility to cleavage by an endonuclease
or exonuclease, such as when the iRNA agent is introduced into the
body of a subject. Methods can be employed to identify sites that
are susceptible to modification, particularly cleavage, e.g.,
cleavage by a component found in the body of a subject.
[0098] When sites susceptible to cleavage are identified, a further
iRNA agent can be designed and/or synthesized wherein the potential
cleavage site is made resistant to cleavage, e.g. by introduction
of a 2'-modification on the site of cleavage, e.g. a 2'-O-methyl
group. This further iRNA agent can be retested for stability, and
this process may be iterated until an iRNA agent is found
exhibiting the desired stability.
[0099] In Vivo Testing
[0100] An iRNA agent identified as being capable of inhibiting ApoB
gene expression can be tested for functionality in vivo in an
animal model (e.g., in a mammal, such as in mouse or rat). For
example, the iRNA agent can be administered to an animal, and the
iRNA agent evaluated with respect to its biodistribution,
stability, and its ability to inhibit ApoB gene expression.
[0101] The iRNA agent can be administered directly to the target
tissue, such as by injection, or the iRNA agent can be administered
to the animal model in the same manner that it would be
administered to a human
[0102] The iRNA agent can also be evaluated for its intracellular
distribution. The evaluation can include determining whether the
iRNA agent was taken up into the cell. The evaluation can also
include determining the stability (e.g., the half-life) of the iRNA
agent. Evaluation of an iRNA agent in vivo can be facilitated by
use of an iRNA agent conjugated to a traceable marker (e.g., a
fluorescent marker such as fluorescein; a radioactive label, such
as .sup.35S, .sup.32P, .sup.33P, or .sup.3H; gold particles; or
antigen particles for immunohistochemistry).
[0103] An iRNA agent useful for monitoring biodistribution can lack
gene silencing activity in vivo. For example, the iRNA agent can
target a gene not present in the animal (e.g., an iRNA agent
injected into mouse can target luciferase), or an iRNA agent can
have a non-sense sequence, which does not target any gene, e.g.,
any endogenous gene). Localization/biodistribution of the iRNA can
be monitored, e.g. by a traceable label attached to the iRNA agent,
such as a traceable agent described above
[0104] The iRNA agent can be evaluated with respect to its ability
to down regulate ApoB gene expression. Levels of ApoB gene
expression in vivo can be measured, for example, by in situ
hybridization, or by the isolation of RNA from tissue prior to and
following exposure to the iRNA agent. Where the animal needs to be
sacrificed in order to harvest the tissue, an untreated control
animal will serve for comparison. Target ApoB mRNA can be detected
by any desired method, including but not limited to RT-PCR,
Northern blot, branched-DNA assay, or RNAase protection assay.
Alternatively, or additionally, ApoB gene expression can be
monitored by performing Western blot analysis on tissue extracts
treated with the iRNA agent.
[0105] iRNA Chemistry
[0106] Described herein are isolated iRNA agents, e.g., RNA
molecules, (double-stranded; single-stranded) that mediate RNAi to
inhibit expression of ApoB.
[0107] RNA agents discussed herein include otherwise unmodified RNA
as well as RNA which have been modified, e.g., to improve efficacy,
and polymers of nucleoside surrogates. Unmodified RNA refers to a
molecule in which the components of the nucleic acid, namely
sugars, bases, and phosphate moieties, are the same or essentially
the same as that which occur in nature, preferably as occur
naturally in the human body. The art has referred to rare or
unusual, but naturally occurring, RNAs as modified RNAs, see, e.g.,
Limbach et al., (1994) Nucleic Acids Res. 22: 2183-2196. Such rare
or unusual RNAs, often termed modified RNAs (apparently because the
are typically the result of a post-transcriptional modification)
are within the term unmodified RNA, as used herein. Modified RNA as
used herein refers to a molecule in which one or more of the
components of the nucleic acid, namely sugars, bases, and phosphate
moieties, are different from that which occur in nature, preferably
different from that which occurs in the human body. While they are
referred to as modified "RNAs," they will of course, because of the
modification, include molecules which are not RNAs. Nucleoside
surrogates are molecules in which the ribophosphate backbone is
replaced with a non-ribophosphate construct that allows the bases
to the presented in the correct spatial relationship such that
hybridization is substantially similar to what is seen with a
ribophosphate backbone, e.g., non-charged mimics of the
ribophosphate backbone. Examples of all of the above are discussed
herein.
[0108] Modifications described herein can be incorporated into any
double-stranded RNA and RNA-like molecule described herein, e.g.,
an iRNA agent. It may be desirable to modify one or both of the
antisense and sense strands of an iRNA agent. As nucleic acids are
polymers of subunits or monomers, many of the modifications
described below occur at a position which is repeated within a
nucleic acid, e.g., a modification of a base, or a phosphate
moiety, or the non-linking O of a phosphate moiety. In some cases
the modification will occur at all of the subject positions in the
nucleic acid but in many, and in fact in most, cases it will not.
By way of example, a modification may only occur at a 3' or 5'
terminal position, may only occur in a terminal region, e.g. at a
position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10
nucleotides of a strand. A modification may occur in a double
strand region, a single strand region, or in both. E.g., a
phosphorothioate modification at a non-linking O position may only
occur at one or both termini, may only occur in a terminal regions,
e.g., at a position on a terminal nucleotide or in the last 2, 3,
4, 5, or 10 nucleotides of a strand, or may occur in double strand
and single strand regions, particularly at termini. Similarly, a
modification may occur on the sense strand, antisense strand, or
both. In some cases, the sense and antisense strand will have the
same modifications or the same class of modifications, but in other
cases the sense and antisense strand will have different
modifications, e.g., in some cases it may be desirable to modify
only one strand, e.g. the sense strand.
[0109] Two prime objectives for the introduction of modifications
into iRNA agents is their stabilization towards degradation in
biological environments and the improvement of pharmacological
properties, e.g. pharmacodynamic properties, which are further
discussed below. Other suitable modifications to a sugar, base, or
backbone of an iRNA agent are described in co-owned PCT Application
No. PCT/US2004/01193, filed Jan. 16, 2004. An iRNA agent can
include a non-naturally occurring base, such as the bases described
in co-owned PCT Application No. PCT/US2004/011822, filed Apr. 16,
2004. An iRNA agent can include a non-naturally occurring sugar,
such as a non-carbohydrate cyclic carrier molecule. Exemplary
features of non-naturally occurring sugars for use in iRNA agents
are described in co-owned PCT Application No. PCT/US2004/11829
filed Apr. 16, 2003.
[0110] An iRNA agent can include an internucleotide linkage (e.g.,
the chiral phosphorothioate linkage) useful for increasing nuclease
resistance. In addition, or in the alternative, an iRNA agent can
include a ribose mimic for increased nuclease resistance. Exemplary
internucleotide linkages and ribose mimics for increased nuclease
resistance are described in co-owned PCT Application No.
PCT/US2004/07070 filed on Mar. 8, 2004.
[0111] An iRNA agent can include ligand-conjugated monomer subunits
and monomers for oligonucleotide synthesis. Exemplary monomers are
described in co-owned U.S. application Ser. No. 10/916,185, filed
on Aug. 10, 2004.
[0112] An iRNA agent can have a ZXY structure, such as is described
in co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8,
2004.
[0113] An iRNA agent can be complexed with an amphipathic moiety.
Exemplary amphipathic moieties for use with iRNA agents are
described in co-owned PCT Application No. PCT/US2004/07070 filed on
Mar. 8, 2004.
[0114] The sense and antisense sequences of an iRNA agent can be
palindromic. Exemplary features of palindromic iRNA agents are
described in co-owned PCT Application No. PCT/US2004/07070 filed on
Mar. 8, 2004.
[0115] In another embodiment, the iRNA agent can be complexed to a
delivery agent that features a modular complex. The complex can
include a carrier agent linked to one or more of (preferably two or
more, more preferably all three of): (a) a condensing agent (e.g.,
an agent capable of attracting, e.g., binding, a nucleic acid,
e.g., through ionic or electrostatic interactions); (b) a fusogenic
agent (e.g., an agent capable of fusing and/or being transported
through a cell membrane); and (c) a targeting group, e.g., a cell
or tissue targeting agent, e.g., a lectin, glycoprotein, lipid or
protein, e.g., an antibody, that binds to a specified cell type.
iRNA agents complexed to a delivery agent are described in co-owned
PCT Application No. PCT/US2004/07070 filed on Mar. 8, 2004.
[0116] An iRNA agent can have non-canonical pairings, such as
between the sense and antisense sequences of the iRNA duplex.
Exemplary features of non-canonical iRNA agents are described in
co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8,
2004.
[0117] Enhanced Nuclease Resistance
[0118] An iRNA agent, e.g., an iRNA agent that targets ApoB, can
have enhanced resistance to nucleases. One way to increase
resistance is to identify cleavage sites and modify such sites to
inhibit cleavage. For example, the dinucleotides 5'-UA-3',
5'-UG-3', 5'-CA-3', 5'-UU-3', or 5'-CC-3' can serve as cleavage
sites, as described in co-owned and co-pending applications U.S.
60/574,744 and PCT/US2005/018931.
[0119] For increased nuclease resistance and/or binding affinity to
the target, an iRNA agent, e.g., the sense and/or antisense strands
of the iRNA agent, can include, for example, 2'-modified ribose
units and/or phosphorothioate linkages. E.g., the 2' hydroxyl group
(OH) can be modified or replaced with a number of different "oxy"
or "deoxy" substituents.
[0120] Examples of "oxy"-2' hydroxyl group modifications include
alkoxy or aryloxy (OR, e.g., R.dbd.H, alkyl, cycloalkyl, aryl,
aralkyl, heteroaryl or sugar); polyethyleneglycols (PEG),
O(CH.sub.2CH.sub.2O).sub.nCH.sub.2CH.sub.2OR; "locked" nucleic
acids (LNA) in which the 2' hydroxyl is connected, e.g., by a
methylene bridge, to the 4' carbon of the same ribose sugar;
O-AMINE (AMINE=NH.sub.2; alkylamino, dialkylamino, heterocyclyl,
arylamino, diaryl amino, heteroaryl amino, or diheteroaryl amino,
ethylene diamine, polyamino) and aminoalkoxy,
O(CH.sub.2).sub.nAMINE, (e.g., AMINE=NH.sub.2; alkylamino,
dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl
amino, or diheteroaryl amino, ethylene diamine, polyamino). It is
noteworthy that oligonucleotides containing only the methoxyethyl
group (MOE), (OCH.sub.2CH.sub.2OCH.sub.3, a PEG derivative),
exhibit nuclease stabilities comparable to those modified with the
robust phosphorothioate modification.
[0121] "Deoxy" modifications include hydrogen (i.e. deoxyribose
sugars, which are of particular relevance to the overhang portions
of partially ds RNA); halo (e.g., fluoro); amino (e.g. NH.sub.2;
alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino,
heteroaryl amino, diheteroaryl amino, or amino acid);
NH(CH.sub.2CH.sub.2NH).sub.nCH.sub.2CH.sub.2-AMINE (AMINE=NH.sub.2;
alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino,
heteroaryl amino, or diheteroaryl amino), --NHC(O)R (R=alkyl,
cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto;
alkyl-thio-alkyl; thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl
and alkynyl, which may be optionally substituted with e.g., an
amino functionality. Preferred substitutents are 2'-methoxyethyl,
2'-OCH3, 2'-O-allyl, 2'-C-allyl, and 2'-fluoro.
[0122] To maximize nuclease resistance, the 2' modifications can be
used in combination with one or more phosphate linker modifications
(e.g., phosphorothioate). The so-called "chimeric" oligonucleotides
are those that contain two or more different modifications.
[0123] In certain embodiments, all the pyrimidines of an iRNA agent
carry a 2'-modification, and the iRNA agent therefore has enhanced
resistance to endonucleases. Enhanced nuclease resistance can also
be achieved by modifying the 5' nucleotide, resulting, for example,
in at least one 5'-uridine-adenine-3' (5'-UA-3') dinucleotide
wherein the uridine is a 2'-modified nucleotide; at least one
5'-uridine-guanine-3' (5'-UG-3') dinucleotide, wherein the
5'-uridine is a 2'-modified nucleotide; at least one
5'-cytidine-adenine-3' (5'-CA-3') dinucleotide, wherein the
5'-cytidine is a 2'-modified nucleotide; at least one
5'-uridine-uridine-3' (5'-UU-3') dinucleotide, wherein the
5'-uridine is a 2'-modified nucleotide; or at least one
5'-cytidine-cytidine-3' (5'-CC-3') dinucleotide, wherein the
5'-cytidine is a 2'-modified nucleotide. The iRNA agent can include
at least 2, at least 3, at least 4 or at least 5 of such
dinucleotides. Preferably, the 5'-most pyrimidines in all
occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3',
and 5'-UG-3' are 2'-modified nucleotides. More preferably, all
pyrimidines in the sense strand are 2'-modified nucleotides, and
the 5'-most pyrimidines in all occurrences of the sequence motifs
5'-UA-3' and 5'-CA-3'. Most preferably, all pyrimidines in the
sense strand are 2'-modified nucleotides, and the 5'-most
pyrimidines in all occurrences of the sequence motifs 5'-UA-3',
5'-CA-3', 5'-UU-3', and 5'-UG-3' are 2'-modified nucleotides in the
antisense strand. The latter patterns of modifications have been
shown by the instant inventors to maximize the contribution of the
nucleotide modifications to the stabilization of the overall
molecule towards nuclease degradation, while minimizing the overall
number of modifications required to a desired stability, see
co-owned and co-pending PCT/US2005/018931, hereby incorporated
herein by reference in its entirety.
[0124] The inclusion of furanose sugars in the oligonucleotide
backbone can also decrease endonucleolytic cleavage. An iRNA agent
can be further modified by including a 3' cationic group, or by
inverting the nucleoside at the 3'-terminus with a 3'-3' linkage.
In another alternative, the 3'-terminus can be blocked with an
aminoalkyl group, e.g., a 3' C5-aminoalkyl dT. Other 3' conjugates
can inhibit 3'-5' exonucleolytic cleavage. While not being bound by
theory, a 3' conjugate, such as naproxen or ibuprofen, may inhibit
exonucleolytic cleavage by sterically blocking the exonuclease from
binding to the 3'-end of oligonucleotide. Even small alkyl chains,
aryl groups, or heterocyclic conjugates or modified sugars
(D-ribose, deoxyribose, glucose etc.) can block
3'-5'-exonucleases.
[0125] Similarly, 5' conjugates can inhibit 5'-3' exonucleolytic
cleavage. While not being bound by theory, a 5' conjugate, such as
naproxen or ibuprofen, may inhibit exonucleolytic cleavage by
sterically blocking the exonuclease from binding to the 5'-end of
oligonucleotide. Even small alkyl chains, aryl groups, or
heterocyclic conjugates or modified sugars (D-ribose, deoxyribose,
glucose etc.) can block 3'-5'-exonucleases.
[0126] An iRNA agent can have increased resistance to nucleases
when a duplexed iRNA agent includes a single-stranded nucleotide
overhang on at least one end. In preferred embodiments, the
nucleotide overhang includes 1 to 4, preferably 2 to 3, unpaired
nucleotides. In a preferred embodiment, the unpaired nucleotide of
the single-stranded overhang that is directly adjacent to the
terminal nucleotide pair contains a purine base, and the terminal
nucleotide pair is a G-C pair, or at least two of the last four
complementary nucleotide pairs are G-C pairs. In further
embodiments, the nucleotide overhang may have 1 or 2 unpaired
nucleotides, and in an exemplary embodiment the nucleotide overhang
is 5'-GC-3'. In preferred embodiments, the nucleotide overhang is
on the 3'-end of the antisense strand. In one embodiment, the iRNA
agent includes the motif 5'-CGC-3' on the 3'-end of the antisense
strand, such that a 2-nt overhang 5'-GC-3' is formed.
[0127] Thus, an iRNA agent can include monomers which have been
modified so as to inhibit degradation, e.g., by nucleases, e.g.,
endonucleases or exonucleases, found in the body of a subject.
These monomers are referred to herein as NRMs, or Nuclease
Resistance promoting Monomers or modifications. In many cases these
modifications will modulate other properties of the iRNA agent as
well, e.g., the ability to interact with a protein, e.g., a
transport protein, e.g., serum albumin, or a member of the RISC, or
the ability of the first and second sequences to form a duplex with
one another or to form a duplex with another sequence, e.g., a
target molecule.
[0128] While not wishing to be bound by theory, it is believed that
modifications of the sugar, base, and/or phosphate backbone in an
iRNA agent can enhance endonuclease and exonuclease resistance, and
can enhance interactions with transporter proteins and one or more
of the functional components of the RISC complex. Preferred
modifications are those that increase exonuclease and endonuclease
resistance and thus prolong the half-life of the iRNA agent prior
to interaction with the RISC complex, but at the same time do not
render the iRNA agent inactive with respect to its intended
activity as a target mRNA cleavage directing agent. Again, while
not wishing to be bound by any theory, it is believed that
placement of the modifications at or near the 3' and/or 5'-end of
antisense strands can result in iRNA agents that meet the preferred
nuclease resistance criteria delineated above. Again, still while
not wishing to be bound by any theory, it is believed that
placement of the modifications at e.g., the middle of a sense
strand can result in iRNA agents that are relatively less likely to
show off-target effects.
[0129] Modifications that can be useful for producing iRNA agents
that meet the preferred nuclease resistance criteria delineated
above can include one or more of the following chemical and/or
stereochemical modifications of the sugar, base, and/or phosphate
backbone:
[0130] (i) chiral (S.sub.P) thioates. Thus, preferred NRMs include
nucleotide dimers with an enriched or pure for a particular chiral
form of a modified phosphate group containing a heteroatom at the
nonbridging position, e.g., Sp or Rp, at the position X, where this
is the position normally occupied by the oxygen. The atom at X can
also be S, Se, Nr.sub.2, or Br.sub.3. When X is S, enriched or
chirally pure Sp linkage is preferred. Enriched means at least 70,
80, 90, 95, or 99% of the preferred form. Such NRMs are discussed
in more detail below;
[0131] (ii) attachment of one or more cationic groups to the sugar,
base, and/or the phosphorus atom of a phosphate or modified
phosphate backbone moiety. Thus, preferred NRMs include monomers at
the terminal position derivatized at a cationic group. As the
5'-end of an antisense sequence should have a terminal --OH or
phosphate group this NRM is preferably not used at the 5'-end of an
antisense sequence. The group should be attached at a position on
the base which minimizes interference with H bond formation and
hybridization, e.g., away form the face which interacts with the
complementary base on the other strand, e.g, at the 5' position of
a pyrimidine or a 7-position of a purine. These are discussed in
more detail below;
[0132] (iii) nonphosphate linkages at the termini. Thus, preferred
NRMs include Non-phosphate linkages, e.g., a linkage of 4 atoms
which confers greater resistance to cleavage than does a phosphate
bond. Examples include 3' CH2-NCH.sub.3--O--CH.sub.2-5' and 3'
CH.sub.2--NH--(O.dbd.)--CH.sub.2-5';
[0133] (iv) 3'-bridging thiophosphates and 5'-bridging
thiophosphates. Thus, preferred NRM's can included these
structures;
[0134] (v) L-RNA, 2'-5' linkages, inverted linkages, a-nucleosides.
Thus, other preferred NRM's include: L nucleosides and dimeric
nucleotides derived from L-nucleosides; 2'-5' phosphate,
non-phosphate and modified phosphate linkages (e.g.,
thiophosphates, phosphoramidates and boronophosphates); dimers
having inverted linkages, e.g., 3'-3' or 5'-5' linkages; monomers
having an alpha linkage at the 1' site on the sugar, e.g., the
structures described herein having an alpha linkage;
[0135] (vi) conjugate groups. Thus, preferred NRM's can include,
e.g., a targeting moiety or a conjugated ligand described herein
conjugated with the monomer, e.g., through the sugar, base, or
backbone;
[0136] (vi) abasic linkages. Thus, preferred NRM's can include an
abasic monomer, e.g., an abasic monomer as described herein (e.g.,
a nucleobaseless monomer); an aromatic or heterocyclic or
polyheterocyclic aromatic monomer as described herein; and
[0137] (vii) 5'-phosphonates and 5'-phosphate prodrugs. Thus,
preferred NRM's include monomers, preferably at the terminal
position, e.g., the 5' position, in which one or more atoms of the
phosphate group is derivatized with a protecting group, which
protecting group or groups, are removed as a result of the action
of a component in the subject's body, e.g, a carboxyesterase or an
enzyme present in the subject's body. E.g., a phosphate prodrug in
which a carboxy esterase cleaves the protected molecule resulting
in the production of a thioate anion which attacks a carbon
adjacent to the O of a phosphate and resulting in the production of
an unprotected phosphate.
[0138] One or more different NRM modifications can be introduced
into an iRNA agent or into a sequence of an iRNA agent. An NRM
modification can be used more than once in a sequence or in an iRNA
agent. As some NRMs interfere with hybridization the total number
incorporated, should be such that acceptable levels of iRNA agent
duplex formation are maintained.
[0139] In some embodiments NRM modifications are introduced into
the terminal cleavage site or in the cleavage region of a sequence
(a sense strand or sequence) which does not target a desired
sequence or gene in the subject. This can reduce off-target
silencing.
[0140] Nuclease resistant modifications include some which can be
placed only at the terminus and others which can go at any
position. Generally the modifications that can inhibit
hybridization so it is preferably to use them only in terminal
regions, and preferable to not use them at the cleavage site or in
the cleavage region of an sequence which targets a subject sequence
or gene. The can be used anywhere in a sense sequence, provided
that sufficient hybridization between the two sequences of the iRNA
agent is maintained. In some embodiments it is desirable to put the
NRM at the cleavage site or in the cleavage region of a sequence
which does not target a subject sequence or gene, as it can
minimize off-target silencing.
[0141] In addition, an iRNA agent described herein can have an
overhang which does not form a duplex structure with the other
sequence of the iRNA agent--it is an overhang, but it does
hybridize, either with itself, or with another nucleic acid, other
than the other sequence of the iRNA agent.
[0142] In most cases, the nuclease-resistance promoting
modifications will be distributed differently depending on whether
the sequence will target a sequence in the subject (often referred
to as an antisense sequence) or will not target a sequence in the
subject (often referred to as a sense sequence). If a sequence is
to target a sequence in the subject, modifications which interfere
with or inhibit endonuclease cleavage should not be inserted in the
region which is subject to RISC mediated cleavage, e.g., the
cleavage site or the cleavage region (As described in Elbashir et
al., 2001, Genes and Dev. 15: 188, hereby incorporated by
reference). Cleavage of the target occurs about in the middle of a
20 or 21 nt guide RNA, or about 10 or 11 nucleotides upstream of
the first nucleotide which is complementary to the guide sequence.
As used herein cleavage site refers to the nucleotide on either
side of the cleavage site, on the target or on the iRNA agent
strand which hybridizes to it. Cleavage region means an nucleotide
with 1, 2, or 3 nucleotides of the cleave site, in either
direction.)
[0143] Such modifications can be introduced into the terminal
regions, e.g., at the terminal position or with 2, 3, 4, or 5
positions of the terminus, of a sequence which targets or a
sequence which does not target a sequence in the subject.
[0144] Tethered Ligands
[0145] The properties of an iRNA agent, including its
pharmacological properties, can be influenced and tailored, for
example, by the introduction of ligands, e.g. tethered ligands.
[0146] A wide variety of entities, e.g., ligands, can be tethered
to an iRNA agent, e.g., to the carrier of a ligand-conjugated
monomer subunit. Examples are described below in the context of a
ligand-conjugated monomer subunit but that is only preferred,
entities can be coupled at other points to an iRNA agent.
[0147] Preferred moieties are ligands, which are coupled,
preferably covalently, either directly or indirectly via an
intervening tether, to the carrier. In preferred embodiments, the
ligand is attached to the carrier via an intervening tether. The
ligand or tethered ligand may be present on the ligand-conjugated
monomer\when the ligand-conjugated monomer is incorporated into the
growing strand. In some embodiments, the ligand may be incorporated
into a "precursor" ligand-conjugated monomer subunit after a
"precursor" ligand-conjugated monomer subunit has been incorporated
into the growing strand. For example, a monomer having, e.g., an
amino-terminated tether, e.g., TAP--(CH.sub.2).sub.nNH.sub.2 may be
incorporated into a growing sense or antisense strand. In a
subsequent operation, i.e., after incorporation of the precursor
monomer subunit into the strand, a ligand having an electrophilic
group, e.g., a pentafluorophenyl ester or aldehyde group, can
subsequently be attached to the precursor ligand-conjugated monomer
by coupling the electrophilic group of the ligand with the terminal
nucleophilic group of the precursor ligand-conjugated monomer
subunit tether.
[0148] In preferred embodiments, a ligand alters the distribution,
targeting or lifetime of an iRNA agent into which it is
incorporated. In preferred embodiments a ligand provides an
enhanced affinity for a selected target, e.g, molecule, cell or
cell type, compartment, e.g., a cellular or organ compartment,
tissue, organ or region of the body, as, e.g., compared to a
species absent such a ligand.
[0149] Preferred ligands can improve transport, hybridization, and
specificity properties and may also improve nuclease resistance of
the resultant natural or modified oligoribonucleotide, or a
polymeric molecule comprising any combination of monomers described
herein and/or natural or modified ribonucleotides.
[0150] Ligands in general can include therapeutic modifiers, e.g.,
for enhancing uptake; diagnostic compounds or reporter groups e.g.,
for monitoring distribution; cross-linking agents;
nuclease-resistance conferring moieties; and natural or unusual
nucleobases. General examples include lipophiles, lipids, steroids
(e.g., uvaol, hecigenin, diosgenin), terpenes (e.g., triterpenes,
e.g., sarsasapogenin, Friedelin, epifriedelanol derivatized
lithocholic acid), vitamins (e.g., folic acid, vitamin A, biotin,
pyridoxal), carbohydrates, proteins, protein binding agents,
integrin targeting molecules, polycationics, peptides, polyamines,
and peptide mimics.
[0151] Ligands can include a naturally occurring substance, (e.g.,
human serum albumin (HSA), low-density lipoprotein (LDL), or
globulin); carbohydrate (e.g., a dextran, pullulan, chitin,
chitosan, inulin, cyclodextrin or hyaluronic acid); amino acid, or
a lipid. The ligand may also be a recombinant or synthetic
molecule, such as a synthetic polymer, e.g., a synthetic polyamino
acid. Examples of polyamino acids include polyamino acid is a
polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid,
styrene-maleic acid anhydride copolymer,
poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic
anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer
(HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA),
polyurethane, poly(2-ethylacryllic acid), N-isopropylacrylamide
polymers, or polyphosphazine. Example of polyamines include:
polyethylenimine, polylysine (PLL), spermine, spermidine,
polyamine, pseudopeptide-polyamine, peptidomimetic polyamine,
dendrimer polyamine, arginine, amidine, protamine, cationic
moieties, e.g., cationic lipid, cationic porphyrin, quaternary salt
of a polyamine, or an alpha helical peptide.
[0152] Ligands can also include targeting groups, e.g., a cell or
tissue targeting agent, e.g., a lectin, glycoprotein, lipid or
protein, e.g., an antibody, that binds to a specified cell type
such as a liver cell or a cell of the jejunum. A targeting group
can be a thyrotropin, melanotropin, lectin, glycoprotein,
surfactant protein A, Mucin carbohydrate, multivalent lactose,
multivalent galactose, N-acetyl-galactosamine,
N-acetyl-gulucosamine multivalent mannose, multivalent fucose,
glycosylated polyaminoacids, multivalent galactose, transferrin,
bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol,
a steroid, bile acid, folate, vitamin B12, biotin, or an RGD
peptide or RGD peptide mimetic.
[0153] Other examples of ligands include dyes, intercalating agents
(e.g. acridines), cross-linkers (e.g. psoralene, mitomycin C),
porphyrins (TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic
hydrocarbons (e.g., phenazine, dihydrophenazine), artificial
endonucleases (e.g. EDTA), lipophilic molecules, e.g, cholesterol,
cholic acid, adamantane acetic acid, 1-pyrene butyric acid,
dihydrotestosterone, glycerol (e.g., esters and ethers thereof,
e.g., C.sub.10, C.sub.11, C.sub.12, C.sub.13, C.sub.14, C.sub.15,
C.sub.16, C.sub.17, C.sub.18, C.sub.19, or C.sub.20 alkyl; e.g.,
1,3-bis-O(hexadecyl)glycerol, 1,3-bis-O(octaadecyl)glycerol),
geranyloxyhexyl group, hexadecylglycerol, borneol, menthol,
1,3-propanediol, heptadecyl group, palmitic acid, myristic acid,
O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid,
dimethoxytrityl, or phenoxazine) and peptide conjugates (e.g.,
antennapedia peptide, Tat peptide), alkylating agents, phosphate,
amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG].sub.2,
polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes,
haptens (e.g. biotin), transport/absorption facilitators (e.g.,
aspirin, vitamin E, folic acid), synthetic ribonucleases (e.g.,
imidazole, bisimidazole, histamine, imidazole clusters,
acridine-imidazole conjugates, Eu3+ complexes of
tetraazamacrocycles), dinitrophenyl, HRP, or AP.
[0154] Ligands can be proteins, e.g., glycoproteins, or peptides,
e.g., molecules having a specific affinity for a co-ligand, or
antibodies e.g., an antibody, that binds to a specified cell type
such as a cancer cell, endothelial cell, or bone cell. Ligands may
also include hormones and hormone receptors. They can also include
non-peptidic species, such as lipids, lectins, carbohydrates,
vitamins, cofactors, multivalent lactose, multivalent galactose,
N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose,
or multivalent fucose. The ligand can be, for example, a
lipopolysaccharide, an activator of p38 MAP kinase, or an activator
of NF-.kappa.B.
[0155] The ligand can be a substance, e.g, a drug, which can
increase the uptake of the iRNA agent into the cell, for example,
by disrupting the cell's cytoskeleton, e.g., by disrupting the
cell's microtubules, microfilaments, and/or intermediate filaments.
The drug can be, for example, taxon, vincristine, vinblastine,
cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin,
swinholide A, indanocine, or myoservin.
[0156] The ligand can increase the uptake of the iRNA agent into
the cell by activating an inflammatory response, for example.
Exemplary ligands that would have such an effect include tumor
necrosis factor alpha (TNFalpha), interleukin-1 beta, or gamma
interferon.
[0157] In one aspect, the ligand is a lipid or lipid-based
molecule. Such a lipid or lipid-based molecule preferably binds a
serum protein, e.g., human serum albumin (HSA). An HSA binding
ligand allows for distribution of the conjugate to a target tissue,
e.g., liver tissue, including parenchymal cells of the liver. Other
molecules that can bind HSA can also be used as ligands. For
example, neproxin or aspirin can be used. A lipid or lipid-based
ligand can (a) increase resistance to degradation of the conjugate,
(b) increase targeting or transport into a target cell or cell
membrane, and/or (c) can be used to adjust binding to a serum
protein, e.g., HSA.
[0158] A lipid based ligand can be used to modulate, e.g., control
the binding of the conjugate to a target tissue. For example, a
lipid or lipid-based ligand that binds to HSA more strongly will be
less likely to be targeted to the kidney and therefore less likely
to be cleared from the body. A lipid or lipid-based ligand that
binds to HSA less strongly can be used to target the conjugate to
the kidney.
[0159] In a preferred embodiment, the lipid based ligand binds HSA.
Preferably, it binds HSA with a sufficient affinity such that the
conjugate will be preferably distributed to a non-kidney tissue.
However, it is preferred that the affinity not be so strong that
the HSA-ligand binding cannot be reversed.
[0160] In another aspect, the ligand is a moiety, e.g., a vitamin,
which is taken up by a target cell, e.g., a proliferating cell.
These are particularly useful for treating disorders characterized
by unwanted cell proliferation, e.g., of the malignant or
non-malignant type, e.g., cancer cells. Exemplary vitamins include
vitamin A, E, and K. Other exemplary vitamins include are B
vitamin, e.g., folic acid, B12, riboflavin, biotin, pyridoxal or
other vitamins or nutrients taken up by cancer cells. Also included
are HSA and low density lipoprotein (LDL).
[0161] In another aspect, the ligand is a cell-permeation agent,
preferably a helical cell-permeation agent. Preferably, the agent
is amphipathic. An exemplary agent is a peptide such as tat or
antennopedia. If the agent is a peptide, it can be modified,
including a peptidylmimetic, invertomers, non-peptide or
pseudo-peptide linkages, and use of D-amino acids. The helical
agent is preferably an alpha-helical agent, which preferably has a
lipophilic and a lipophobic phase.
[0162] Peptides that target markers enriched in proliferating cells
can be used. E.g., RGD containing peptides and petomimetics can
target cancer cells, in particular cells that exhibit an
I.sub.v.theta..sub.3 integrin. Thus, one could use RGD peptides,
cyclic peptides containing RGD, RGD peptides that include D-amino
acids, as well as synthetic RGD mimics. In addition to RGD, one can
use other moieties that target the I.sub.v-.theta..sub.3 integrin
ligand. Generally, such ligands can be used to control
proliferating cells and angiogeneis. Preferred conjugates of this
type include an iRNA agent that targets PECAM-1, VEGF, or other
cancer gene, e.g., a cancer gene described herein.
[0163] A targeting agent that incorporates a sugar, e.g., galactose
and/or analogues thereof, is particularly useful. These agents
target, in particular, the parenchymal cells of the liver. For
example, a targeting moiety can include more than one or preferably
two or three galactose moieties, spaced about 15 angstroms from
each other. The targeting moiety can alternatively be lactose
(e.g., three lactose moieties), which is glucose coupled to a
galactose. The targeting moiety can also be N-Acetyl-Galactosamine,
N--Ac-Glucosamine. A mannose or mannose-6-phosphate targeting
moiety can be used for macrophage targeting.
[0164] The ligand can be a peptide or peptidomimetic. A
peptidomimetic (also referred to herein as an oligopeptidomimetic)
is a molecule capable of folding into a defined three-dimensional
structure similar to a natural peptide. The attachment of peptide
and peptidomimetics to iRNA agents can affect pharmacokinetic
distribution of the iRNA, such as by enhancing cellular recognition
and absorption. The peptide or peptidomimetic moiety can be about
5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40,
45, or 50 amino acids long.
[0165] iRNA Conjugates
[0166] An iRNA agent can be coupled, e.g., covalently coupled, to a
second agent. For example, an iRNA agent used to treat a particular
disorder, such as a lipid disorder, can be coupled to a second
therapeutic agent, e.g., an agent other than the iRNA agent. The
second therapeutic agent can be one which is directed to the
treatment of the same disorder.
[0167] 5'-Phosphate Modifications
[0168] In preferred embodiments, iRNA agents are 5' phosphorylated
or include a phosphoryl analog at the 5' prime terminus.
5'-phosphate modifications of the antisense strand include those
which are compatible with RISC mediated gene silencing. Suitable
modifications include: 5'-monophosphate ((HO).sub.2(O)P--O-5');
5'-diphosphate ((HO).sub.2(O)P--O--P(HO)(O)--O-5'); 5'-triphosphate
((HO).sub.2(O)P--O--(HO)(O)P--O--P(HO)(O)--O-5'); 5'-guanosine cap
(7-methylated or non-methylated)
(7m-G-O-5'-(HO)(O)P--O--(HO)(O)P--O--P(HO)(O)--O-5'); 5'-adenosine
cap (Appp), and any modified or unmodified nucleotide cap structure
(N--O-5'-(HO)(O)P--O--(HO)(O)P--O--P(HO)(O)--O-5');
5'-monothiophosphate (phosphorothioate; (HO).sub.2(S)P--O-5');
5'-monodithiophosphate (phosphorodithioate; (HO)(HS)(S)P--O-5'),
5'-phosphorothiolate ((HO).sub.2(O)P--S-5'); any additional
combination of oxygen/sulfur replaced monophosphate, diphosphate
and triphosphates (e.g. 5'-alpha-thiotriphosphate,
5'-gamma-thiotriphosphate, etc.), 5'-phosphoramidates
((HO).sub.2(O)P--NH-5', (HO)(NH2)(O)P--O-5'), 5'-alkylphosphonates
(R=alkyl=methyl, ethyl, isopropyl, propyl, etc., e.g.
RP(OH)(O)--O-5'-, (OH).sub.2(O)P-5'-CH2-),
5'-alkyletherphosphonates (R=alkylether=methoxymethyl (MeOCH2-),
ethoxymethyl, etc., e.g. RP(OH)(O)--O-5'-).
[0169] The sense strand can be modified in order to inactivate the
sense strand and prevent formation of an active RISC, thereby
potentially reducing off-target effects. This can be accomplished
by a modification which prevents 5'-phosphorylation of the sense
strand, e.g., by modification with a 5'-O-methyl ribonucleotide
(see Nykanen et al., (2001) ATP requirements and small interfering
RNA structure in the RNA interference pathway. Cell 107, 309-321.)
Other modifications which prevent phosphorylation can also be used,
e.g., simply substituting the 5'-OH by H rather than O-Me.
Alternatively, a large bulky group may be added to the 5'-phosphate
turning it into a phosphodiester linkage.
[0170] Delivery of iRNA Agents to Tissues and Cells
[0171] Targeting to the Liver
[0172] The iRNA agent that targets ApoB can be targeted to the
liver, for example by associating, e.g., conjugating the iRNA agent
to a lipophilic moiety, e.g., a lipid, oleyl, retinyl, or
cholesteryl residue. Conjugation to cholesterol is preferred. Other
lipophilic moieties that can be associated, e.g., conjugated with
the iRNA agent include cholic acid, adamantane acetic acid,
1-pyrene butyric acid, dihydrotestosterone,
1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group,
hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl
group, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid,
O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine.
Alternatively, the iRNA agent can be targeted to the liver by
associating, e.g., conjugating, the iRNA agent to a low-density
lipoprotein (LDL), e.g., a lactosylated LDL, or the iRNA agent can
be targeted to the liver by associating, e.g., conjugating, the
iRNA agent to a polymeric carrier complex with sugar residues.
[0173] The iRNA agent can be targeted to the liver by associating,
e.g., conjugating, the iRNA agent to a liposome complexed with
sugar residues. A targeting agent that incorporates a sugar, e.g.,
galactose and/or analogues thereof, is particularly useful. These
agents target, in particular, the parenchymal cells of the liver.
Preferably, the targeting moiety includes more than one galactose
moiety, more preferably two or three. Most preferably, the
targeting moiety includes three galactose moieties, e.g., spaced
about 15 angstroms from each other. The targeting moiety can be
lactose. A lactose is a glucose coupled to a galactose. Preferably,
the targeting moiety includes three lactoses. The targeting moiety
can also be N-Acetyl-Galactosamine, N--Ac-Glucosamine. A mannose,
or mannose-6-phosphate targeting moiety can be used for macrophage
targeting.
[0174] An iRNA agent can also be targeted to the liver by
association with a low-density lipoprotein (LDL), such as
lactosylated LDL. Polymeric carriers complexed with sugar residues
can also function to target iRNA agents to the liver.
[0175] The targeting agent can be linked directly, e.g., covalently
or non covalently, to the iRNA agent, or to another delivery or
formulation modality, e.g., a liposome. E.g., the iRNA agents with
or without a targeting moiety can be incorporated into a delivery
modality, e.g., a liposome, with or without a targeting moiety.
[0176] The iRNA agent that targets ApoB can be targeted to the
liver, for example by associating, e.g., conjugating the iRNA
agent, to a serum albumin (SA) molecule, e.g., a human serum
albumin (HSA) molecule, or a fragment thereof. The iRNA agent or
composition thereof can have an affinity for an SA, e.g., HSA,
which is sufficiently high such that its levels in the liver are at
least 10, 20, 30, 50, or 100% greater in the presence of SA, e.g.,
HSA, or is such that addition of exogenous SA will increase
delivery to the liver. These criteria can be measured, e.g., by
testing distribution in a mouse in the presence or absence of
exogenous mouse or human SA.
[0177] The SA, e.g., HSA, targeting agent can be linked directly,
e.g., covalently or non-covalently, to the iRNA agent, or to
another delivery or formulation modality, e.g., a liposome. E.g.,
the iRNA agents with or without a targeting moiety can be
incorporated into a delivery modality, e.g., a liposome, with or
without a targeting moiety.
[0178] Transport of iRNA Agents into Cells
[0179] Not wishing to be bound by any theory, the chemical
similarity between cholesterol-conjugated iRNA agents and certain
constituents of lipoproteins (e.g. cholesterol, cholesteryl esters,
phospholipids) may lead to the association of iRNA agents with
lipoproteins (e.g. LDL, HDL) in blood and/or the interaction of the
iRNA agent with cellular components having an affinity for
cholesterol, e.g. components of the cholesterol transport pathway.
Lipoproteins as well as their constituents are taken up and
processed by cells by various active and passive transport
mechanisms, for example, without limitation, endocytosis of
LDL-receptor bound LDL, endocytosis of oxidized or otherwise
modified LDLs through interaction with Scavenger receptor A,
Scavenger receptor B1-mediated uptake of HDL cholesterol in the
liver, pinocytosis, or transport of cholesterol across membranes by
ABC (ATP-binding cassette) transporter proteins, e.g. ABC-A1,
ABC-G1 or ABC-G4. Hence, cholesterol-conjugated iRNA agents could
enjoy facilitated uptake by cells possessing such transport
mechanisms, e.g. cells of the liver. As such, the present invention
provides evidence and general methods for targeting IRNA agents to
cells expressing certain cell surface components, e.g. receptors,
by conjugating a natural ligand for such component (e.g.
cholesterol) to the iRNA agent, or by conjugating a chemical moiety
(e.g. cholesterol) to the iRNA agent which associates with or binds
to a natural ligand for the component (e.g. LDL, HDL).
Other Embodiments
[0180] An RNA, e.g., an iRNA agent, can be produced in a cell in
vivo, e.g., from exogenous DNA templates that are delivered into
the cell. For example, the DNA templates can be inserted into
vectors and used as gene therapy vectors. Gene therapy vectors can
be delivered to a subject by, for example, intravenous injection,
local administration (U.S. Pat. No. 5,328,470), or by stereotactic
injection (see, e.g., Chen et al., Proc. Natl. Acad. Sci. USA
91:3054-3057, 1994). The pharmaceutical preparation of the gene
therapy vector can include the gene therapy vector in an acceptable
diluent, or can comprise a slow release matrix in which the gene
delivery vehicle is imbedded. The DNA templates, for example, can
include two transcription units, one that produces a transcript
that includes the top strand of an iRNA agent and one that produces
a transcript that includes the bottom strand of an iRNA agent. When
the templates are transcribed, the iRNA agent is produced, and
processed into siRNA agent fragments that mediate gene
silencing.
[0181] Physiological Effects
[0182] The iRNA agents described herein can be designed such that
determining therapeutic toxicity is made easier by the
complementarity of the iRNA agent with both a human and a non-human
animal sequence. By these methods, an iRNA agent can consist of a
sequence that is fully complementary to a nucleic acid sequence
from a human and a nucleic acid sequence from at least one
non-human animal, e.g., a non-human mammal, such as a rodent,
ruminant or primate. For example, the non-human mammal can be a
mouse, rat, dog, pig, goat, sheep, cow, monkey, Pan paniscus, Pan
troglodytes, Macaca mulatto, or Cynomolgus monkey. The sequence of
the iRNA agent could be complementary to sequences within
homologous genes, e.g., oncogenes or tumor suppressor genes, of the
non-human mammal and the human. By determining the toxicity of the
iRNA agent in the non-human mammal, one can extrapolate the
toxicity of the iRNA agent in a human. For a more strenuous
toxicity test, the iRNA agent can be complementary to a human and
more than one, e.g., two or three or more, non-human animals.
[0183] The methods described herein can be used to correlate any
physiological effect of an iRNA agent on a human, e.g., any
unwanted effect, such as a toxic effect, or any positive, or
desired effect.
[0184] iRNA Production
[0185] An iRNA can be produced, e.g., in bulk, by a variety of
methods. Exemplary methods include: organic synthesis and RNA
cleavage, e.g., in vitro cleavage.
[0186] Organic Synthesis.
[0187] An iRNA can be made by separately synthesizing each
respective strand of a double-stranded RNA molecule. The component
strands can then be annealed.
[0188] A large bioreactor, e.g., the OligoPilot II from Pharmacia
Biotec AB (Uppsala Sweden), can be used to produce a large amount
of a particular RNA strand for a given iRNA. The OligoPilotII
reactor can efficiently couple a nucleotide using only a 1.5 molar
excess of a phosphoramidite nucleotide. To make an RNA strand,
ribonucleotides amidites are used. Standard cycles of monomer
addition can be used to synthesize the oligonucleotide strands for
the iRNA. Typically, the two complementary strands are produced
separately and then annealed, e.g., after release from the solid
support and deprotection.
[0189] Organic synthesis can be used to produce a discrete iRNA
species. The complementarity of the species to the ApoB gene can be
precisely specified. For example, the species may be complementary
to a region that includes a polymorphism, e.g., a single nucleotide
polymorphism. Further the location of the polymorphism can be
precisely defined. In some embodiments, the polymorphism is located
in an internal region, e.g., at least 4, 5, 7, or 9 nucleotides
from one or both of the termini.
[0190] dsRNA Cleavage.
[0191] iRNAs can also be made by cleaving a larger ds iRNA. The
cleavage can be mediated in vitro or in vivo. For example, to
produce iRNAs by cleavage in vitro, the following method can be
used:
[0192] In vitro transcription. dsRNA is produced by transcribing a
nucleic acid (DNA) segment in both directions. For example, the
HiScribe.TM. RNAi transcription kit (New England Biolabs) provides
a vector and a method for producing a dsRNA for a nucleic acid
segment that is cloned into the vector at a position flanked on
either side by a T7 promoter. Separate templates are generated for
T7 transcription of the two complementary strands for the dsRNA.
The templates are transcribed in vitro by addition of T7 RNA
polymerase and dsRNA is produced. Similar methods using PCR and/or
other RNA polymerases (e.g., T3 or SP6 polymerase) can also be
used. In one embodiment, RNA generated by this method is carefully
purified to remove endotoxins that may contaminate preparations of
the recombinant enzymes.
[0193] In vitro cleavage. dsRNA is cleaved in vitro into iRNAs, for
example, using a Dicer or comparable RNAse III-based activity. For
example, the dsRNA can be incubated in an in vitro extract from
Drosophila or using purified components, e.g. a purified RNAse or
RISC complex. See, e.g., Ketting et al. Genes Dev 2001 Oct. 15;
15(20):2654-9. and Hammond Science 2001 Aug. 10;
293(5532):1146-50.
[0194] dsRNA cleavage generally produces a plurality of iRNA
species, each being a particular 21 to 23 nt fragment of a source
dsRNA molecule. For example, iRNAs that include sequences
complementary to overlapping regions and adjacent regions of a
source dsRNA molecule may be present.
[0195] Regardless of the method of synthesis, the iRNA preparation
can be prepared in a solution (e.g., an aqueous and/or organic
solution) that is appropriate for formulation. For example, the
iRNA preparation can be precipitated and redissolved in pure
double-distilled water, and lyophilized. The dried iRNA can then be
resuspended in a solution appropriate for the intended formulation
process.
[0196] Synthesis of modified and nucleotide surrogate iRNA agents
is discussed below.
[0197] Formulation
[0198] The iRNA agents described herein can be formulated for
administration to a subject.
[0199] For ease of exposition, the formulations, compositions, and
methods in this section are discussed largely with regard to
unmodified iRNA agents. It should be understood, however, that
these formulations, compositions, and methods can be practiced with
other iRNA agents, e.g., modified iRNA agents, and such practice is
within the invention.
[0200] A formulated iRNA composition can assume a variety of
states. In some examples, the composition is at least partially
crystalline, uniformly crystalline, and/or anhydrous (e.g., less
than 80, 50, 30, 20, or 10% water). In another example, the iRNA is
in an aqueous phase, e.g., in a solution that includes water.
[0201] The aqueous phase or the crystalline compositions can, e.g.,
be incorporated into a delivery vehicle, e.g., a liposome
(particularly for the aqueous phase) or a particle (e.g., a
microparticle as can be appropriate for a crystalline composition).
Generally, the iRNA composition is formulated in a manner that is
compatible with the intended method of administration.
[0202] In particular embodiments, the composition is prepared by at
least one of the following methods: spray drying, lyophilization,
vacuum drying, evaporation, fluid bed drying, or a combination of
these techniques; or sonication with a lipid, freeze-drying,
condensation and other self-assembly.
[0203] An iRNA preparation can be formulated in combination with
another agent, e.g., another therapeutic agent or an agent that
stabilizes a iRNA, e.g., a protein that complexes with iRNA to form
an iRNP. Still other agents include chelators, e.g., EDTA (e.g., to
remove divalent cations such as Mg.sup.2+), salts, RNAse inhibitors
(e.g., a broad specificity RNAse inhibitor such as RNAsin) and so
forth.
[0204] In one embodiment, the iRNA preparation includes another
iRNA agent, e.g., a second iRNA agent that can mediate RNAi with
respect to a second gene, or with respect to the same gene. Still
other preparations can include at least three, five, ten, twenty,
fifty, or a hundred or more different iRNA species. Such iRNAs can
mediated RNAi with respect to a similar number of different
genes.
[0205] In one embodiment, the iRNA preparation includes at least a
second therapeutic agent (e.g., an agent other than an RNA or a
DNA).
[0206] In some embodiments, an iRNA agent, e.g., a double-stranded
iRNA agent, or siRNA agent, (e.g., a precursor, e.g., a larger iRNA
agent which can be processed into an siRNA agent, or a DNA which
encodes an iRNA agent, e.g., a double-stranded iRNA agent, or siRNA
agent, or precursor thereof) is formulated to target a particular
cell. For example, a liposome or particle or other structure that
includes a iRNA can also include a targeting moiety that recognizes
a specific molecule on a target cell. The targeting moiety can be a
molecule with a specific affinity for a target cell. Targeting
moieties can include antibodies directed against a protein found on
the surface of a target cell, or the ligand or a receptor-binding
portion of a ligand for a molecule found on the surface of a target
cell.
[0207] In one embodiment, the targeting moiety is attached to a
liposome. For example, U.S. Pat. No. 6,245,427 describes a method
for targeting a liposome using a protein or peptide. In another
example, a cationic lipid component of the liposome is derivatized
with a targeting moiety. For example, WO 96/37194 describes
converting N-glutaryldioleoylphosphatidyl ethanolamine to a
N-hydroxysuccinimide activated ester. The product was then coupled
to an RGD peptide. Additional targeting methods are described
elsewhere herein.
[0208] Treatment Methods and Routes of Delivery
[0209] A composition that includes an iRNA agent, e.g., an iRNA
agent that targets ApoB, can be delivered to a subject by a variety
of routes. Exemplary routes include intrathecal, parenchymal,
intravenous, nasal, oral, and ocular delivery. An iRNA agent can be
incorporated into pharmaceutical compositions suitable for
administration. For example, compositions can include one or more
species of an iRNA agent and a pharmaceutically acceptable carrier.
As used herein the language "pharmaceutically acceptable carrier"
is intended to include any and all solvents, dispersion media,
coatings, antibacterial and antifungal agents, isotonic and
absorption delaying agents, and the like, compatible with
pharmaceutical administration. The use of such media and agents for
pharmaceutically active substances is well known in the art. Except
insofar as any conventional media or agent is incompatible with the
active compound, use thereof in the compositions is contemplated.
Supplementary active compounds can also be incorporated into the
compositions.
[0210] The pharmaceutical compositions of the present invention may
be administered in a number of ways depending upon whether local or
systemic treatment is desired and upon the area to be treated.
Administration may be topical (including ophthalmic, intranasal,
transdermal), oral or parenteral. Parenteral administration
includes intravenous drip, subcutaneous, intraperitoneal or
intramuscular injection, or intrathecal or intraventricular
administration.
[0211] The route of delivery can be dependent on the disorder of
the patient.
[0212] In general, an iRNA agent can be administered by any
suitable method. As used herein, topical delivery can refer to the
direct application of an iRNA agent to any surface of the body,
including the eye, a mucous membrane, surfaces of a body cavity, or
to any internal surface. Formulations for topical administration
may include transdermal patches, ointments, lotions, creams, gels,
drops, sprays, and liquids. Conventional pharmaceutical carriers,
aqueous, powder or oily bases, thickeners and the like may be
necessary or desirable. Topical administration can also be used as
a means to selectively deliver the iRNA agent to the epidermis or
dermis of a subject, or to specific strata thereof, or to an
underlying tissue.
[0213] Compositions for intrathecal or intraventricular
administration may include sterile aqueous solutions which may also
contain buffers, diluents and other suitable additives.
[0214] Formulations for parenteral administration may include
sterile aqueous solutions which may also contain buffers, diluents
and other suitable additives. Intraventricular injection may be
facilitated by an intraventricular catheter, for example, attached
to a reservoir. For intravenous use, the total concentration of
solutes should be controlled to render the preparation
isotonic.
[0215] An iRNA agent can be administered to a subject by pulmonary
delivery. Pulmonary delivery compositions can be delivered by
inhalation by the patient of a dispersion so that the composition,
preferably iRNA, within the dispersion can reach the lung where it
can be readily absorbed through the alveolar region directly into
blood circulation. Pulmonary delivery can be effective both for
systemic delivery and for localized delivery to treat diseases of
the lungs.
[0216] Pulmonary delivery can be achieved by different approaches,
including the use of nebulized, aerosolized, micellular and dry
powder-based formulations. Delivery can be achieved with liquid
nebulizers, aerosol-based inhalers, and dry powder dispersion
devices. Metered-dose devices are preferred. One of the benefits of
using an atomizer or inhaler is that the potential for
contamination is minimized because the devices are self contained.
Dry powder dispersion devices, for example, deliver drugs that may
be readily formulated as dry powders. An iRNA composition may be
stably stored as lyophilized or spray-dried powders by itself or in
combination with suitable powder carriers. The delivery of a
composition for inhalation can be mediated by a dosing timing
element which can include a timer, a dose counter, time measuring
device, or a time indicator which when incorporated into the device
enables dose tracking, compliance monitoring, and/or dose
triggering to a patient during administration of the aerosol
medicament.
[0217] An iRNA agent can be modified such that it is capable of
traversing the blood brain barrier. For example, the iRNA agent can
be conjugated to a molecule that enables the agent to traverse the
barrier. Such modified iRNA agents can be administered by any
desired method, such as by intraventricular or intramuscular
injection, or by pulmonary delivery, for example.
[0218] An iRNA agent can be administered ocularly, such as to treat
retinal disorder, e.g., a retinopathy. For example, the
pharmaceutical compositions can be applied to the surface of the
eye or nearby tissue, e.g., the inside of the eyelid. They can be
applied topically, e.g., by spraying, in drops, as an eyewash, or
an ointment. Ointments or droppable liquids may be delivered by
ocular delivery systems known in the art such as applicators or eye
droppers. Such compositions can include mucomimetics such as
hyaluronic acid, chondroitin sulfate, hydroxypropyl methylcellulose
or poly(vinyl alcohol), preservatives such as sorbic acid, EDTA or
benzylchronium chloride, and the usual quantities of diluents
and/or carriers. The pharmaceutical composition can also be
administered to the interior of the eye, and can be introduced by a
needle or other delivery device which can introduce it to a
selected area or structure. The composition containing the iRNA
agent can also be applied via an ocular patch.
[0219] An iRNA agent can be administered by an oral or nasal
delivery. For example, drugs administered through these membranes
have a rapid onset of action, provide therapeutic plasma levels,
avoid first pass effect of hepatic metabolism, and avoid exposure
of the drug to the hostile gastrointestinal (GI) environment.
Additional advantages include easy access to the membrane sites so
that the drug can be applied, localized and removed easily.
[0220] Administration can be provided by the subject or by another
person, e.g., a another caregiver. A caregiver can be any entity
involved with providing care to the human: for example, a hospital,
hospice, doctor's office, outpatient clinic; a healthcare worker
such as a doctor, nurse, or other practitioner; or a spouse or
guardian, such as a parent. The medication can be provided in
measured doses or in a dispenser which delivers a metered dose.
[0221] The subject can also be monitored for an improvement or
stabilization of disease symptoms.
[0222] The term "therapeutically effective amount" is the amount
present in the composition that is needed to provide the desired
level of drug in the subject to be treated to give the anticipated
physiological response.
[0223] The term "physiologically effective amount" is that amount
delivered to a subject to give the desired palliative or curative
effect.
[0224] The term "pharmaceutically acceptable carrier" means that
the carrier can be taken into the lungs with no significant adverse
toxicological effects on the lungs.
[0225] The types of pharmaceutical excipients that are useful as
carrier include stabilizers such as human serum albumin (HSA),
bulking agents such as carbohydrates, amino acids and polypeptides;
pH adjusters or buffers; salts such as sodium chloride; and the
like. These carriers may be in a crystalline or amorphous form or
may be a mixture of the two.
[0226] Bulking agents that are particularly valuable include
compatible carbohydrates, polypeptides, amino acids or combinations
thereof. Suitable carbohydrates include monosaccharides such as
galactose, D-mannose, sorbose, and the like; disaccharides, such as
lactose, trehalose, and the like; cyclodextrins, such as
2-hydroxypropyl-.beta.-cyclodextrin; and polysaccharides, such as
raffinose, maltodextrins, dextrans, and the like; alditols, such as
mannitol, xylitol, and the like. A preferred group of carbohydrates
includes lactose, threhalose, raffinose maltodextrins, and
mannitol. Suitable polypeptides include aspartame. Amino acids
include alanine and glycine, with glycine being preferred.
[0227] Suitable pH adjusters or buffers include organic salts
prepared from organic acids and bases, such as sodium citrate,
sodium ascorbate, and the like; sodium citrate is preferred.
[0228] In one embodiment, unit doses or measured doses of a
composition that include iRNA are dispensed by an implanted device.
The device can include a sensor that monitors a parameter within a
subject. For example, the device can include a pump, such as an
osmotic pump and, optionally, associated electronics.
[0229] An iRNA agent can be packaged in a viral natural capsid or
in a chemically or enzymatically produced artificial capsid or
structure derived therefrom.
[0230] Dosage. An iRNA agent can be administered at a unit dose
less than about 75 mg per kg of bodyweight, or less than about 70,
60, 50, 40, 30, 20, 10, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.005,
0.001, or 0.0005 mg per kg of bodyweight, and less than 200 nmole
of RNA agent (e.g., about 4.4.times.1016 copies) per kg of
bodyweight, or less than 1500, 750, 300, 150, 75, 15, 7.5, 1.5,
0.75, 0.15, 0.075, 0.015, 0.0075, 0.0015, 0.00075, 0.00015 nmole of
RNA agent per kg of bodyweight. The unit dose, for example, can be
administered by injection (e.g., intravenous or intramuscular,
intrathecally, or directly into an organ), an inhaled dose, or a
topical application.
[0231] Delivery of an iRNA agent directly to an organ (e.g.,
directly to the liver) can be at a dosage on the order of about
0.00001 mg to about 3 mg per organ, or preferably about
0.0001-0.001 mg per organ, about 0.03-3.0 mg per organ, about
0.1-3.0 mg per eye or about 0.3-3.0 mg per organ.
[0232] The dosage can be an amount effective to treat or prevent a
disease or disorder.
[0233] In one embodiment, the unit dose is administered less
frequently than once a day, e.g., less than every 2, 4, 8 or 30
days. In another embodiment, the unit dose is not administered with
a frequency (e.g., not a regular frequency). For example, the unit
dose may be administered a single time.
[0234] In one embodiment, the effective dose is administered with
other traditional therapeutic modalities.
[0235] In one embodiment, a subject is administered an initial
dose, and one or more maintenance doses of an iRNA agent, e.g., a
double-stranded iRNA agent, or siRNA agent, (e.g., a precursor,
e.g., a larger iRNA agent which can be processed into an siRNA
agent, or a DNA which encodes an iRNA agent, e.g., a
double-stranded iRNA agent, or siRNA agent, or precursor thereof).
The maintenance dose or doses are generally lower than the initial
dose, e.g., one-half less of the initial dose. A maintenance
regimen can include treating the subject with a dose or doses
ranging from 0.01 .mu.g to 75 mg/kg of body weight per day, e.g.,
70, 60, 50, 40, 30, 20, 10, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.005,
0.001, or 0.0005 mg per kg of bodyweight per day. The maintenance
doses are preferably administered no more than once every 5, 10, or
30 days. Further, the treatment regimen may last for a period of
time which will vary depending upon the nature of the particular
disease, its severity and the overall condition of the patient. In
preferred embodiments the dosage may be delivered no more than once
per day, e.g., no more than once per 24, 36, 48, or more hours,
e.g., no more than once every 5 or 8 days. Following treatment, the
patient can be monitored for changes in his condition and for
alleviation of the symptoms of the disease state. The dosage of the
compound may either be increased in the event the patient does not
respond significantly to current dosage levels, or the dose may be
decreased if an alleviation of the symptoms of the disease state is
observed, if the disease state has been ablated, or if undesired
side-effects are observed.
[0236] The effective dose can be administered in a single dose or
in two or more doses, as desired or considered appropriate under
the specific circumstances. If desired to facilitate repeated or
frequent infusions, implantation of a delivery device, e.g., a
pump, semi-permanent stent (e.g., intravenous, intraperitoneal,
intracisternal or intracapsular), or reservoir may be
advisable.
[0237] In one embodiment, the iRNA agent pharmaceutical composition
includes a plurality of iRNA agent species. The iRNA agent species
can have sequences that are non-overlapping and non-adjacent with
respect to a naturally occurring target sequence, e.g., a target
sequence of the ApoB gene. In another embodiment, the plurality of
iRNA agent species is specific for different naturally occurring
target genes. For example, an iRNA agent that targets ApoB can be
present in the same pharmaceutical composition as an iRNA agent
that targets a different gene. In another embodiment, the iRNA
agents are specific for different alleles.
[0238] Following successful treatment, it may be desirable to have
the patient undergo maintenance therapy to prevent the recurrence
of the disease state, wherein the compound of the invention is
administered in maintenance doses, ranging from 0.01 .mu.g to 100 g
per kg of body weight (see U.S. Pat. No. 6,107,094).
[0239] The concentration of the iRNA agent composition is an amount
sufficient to be effective in treating or preventing a disorder or
to regulate a physiological condition in humans. The concentration
or amount of iRNA agent administered will depend on the parameters
determined for the agent and the method of administration, e.g.
nasal, buccal, or pulmonary. For example, nasal formulations tend
to require much lower concentrations of some ingredients in order
to avoid irritation or burning of the nasal passages. It is
sometimes desirable to dilute an oral formulation up to 10-100
times in order to provide a suitable nasal formulation.
[0240] Certain factors may influence the dosage required to
effectively treat a subject, including but not limited to the
severity of the disease or disorder, previous treatments, the
general health and/or age of the subject, and other diseases
present. Moreover, treatment of a subject with a therapeutically
effective amount of an iRNA agent, e.g., a double-stranded iRNA
agent, or siRNA agent (e.g., a precursor, e.g., a larger iRNA agent
which can be processed into an siRNA agent, or a DNA which encodes
an iRNA agent, e.g., a double-stranded iRNA agent, or siRNA agent,
or precursor thereof) can include a single treatment or,
preferably, can include a series of treatments. It will also be
appreciated that the effective dosage of an iRNA agent such as an
siRNA agent used for treatment may increase or decrease over the
course of a particular treatment. Changes in dosage may result and
become apparent from the results of diagnostic assays as described
herein. For example, the subject can be monitored after
administering an iRNA agent composition. Based on information from
the monitoring, an additional amount of the iRNA agent composition
can be administered.
[0241] Dosing is dependent on severity and responsiveness of the
disease condition to be treated, with the course of treatment
lasting from several days to several months, or until a cure is
effected or a diminution of disease state is achieved. Optimal
dosing schedules can be calculated from measurements of drug
accumulation in the body of the patient. Persons of ordinary skill
can easily determine optimum dosages, dosing methodologies and
repetition rates. Optimum dosages may vary depending on the
relative potency of individual compounds, and can generally be
estimated based on EC50s found to be effective in in vitro and in
vivo animal models. In some embodiments, the animal models include
transgenic animals that express a human gene, e.g., a gene that
produces a target ApoB RNA. The transgenic animal can be deficient
for the corresponding endogenous RNA. In another embodiment, the
composition for testing includes an iRNA agent that is
complementary, at least in an internal region, to a sequence that
is conserved between the target ApoB RNA in the animal model and
the target ApoB RNA in a human.
[0242] The invention is further illustrated by the following
examples, which should not be construed as further limiting.
EXAMPLES
Example 1
siRNAs were Produced by Solid-Phase Synthesis
[0243] Source of Reagents
[0244] Where the source of a reagent is not specifically given
herein, such reagent may be obtained from any supplier of reagents
for molecular biology at a quality/purity standard for application
in molecular biology.
[0245] sIRNA Synthesis
[0246] Single-stranded RNAs were produced by solid phase synthesis
on a scale of 1 .mu.mole using an Expedite 8909 synthesizer
(Applied Biosystems, Applera Deutschland GmbH, Darmstadt, Germany)
and controlled pore glass (CPG, 500 .ANG., Glen Research, Sterling
Va.) as solid support. RNA and RNA containing 2'-O-methyl
nucleotides were generated by solid phase synthesis employing the
corresponding phosphoramidites and 2'-O-methyl phosphoramidites,
respectively (Proligo Biochemie GmbH, Hamburg, Germany). These
building blocks were incorporated at selected sites within the
sequence of the oligoribonucleotide chain using standard nucleoside
phosphoramidite chemistry such as described in Current protocols in
nucleic acid chemistry, Beaucage, S. L. et al. (Edrs.), John Wiley
& Sons, Inc., New York, N.Y., USA. Phosphorothioate linkages
were introduced by replacement of the iodine oxidizer solution with
a solution of the Beaucage reagent (Chruachem Ltd, Glasgow, UK) in
acetonitrile (1%). Further ancillary reagents were obtained from
Mallinckrodt Baker (Griesheim, Germany).
[0247] Deprotection and purification by anion exchange HPLC of the
crude oligoribonucleotides were carried out according to
established procedures. Yields and concentrations were determined
by UV absorption of a solution of the respective RNA at a
wavelength of 260 nm using a spectral photometer (DU 640B, Beckman
Coulter GmbH, Unterschlei.beta.heim, Germany). Double stranded RNA
was generated by mixing an equimolar solution of complementary
strands in annealing buffer (20 mM sodium phosphate, pH 6.8; 100 mM
sodium chloride), heated in a water bath at 85-90.degree. C. for 3
minutes and cooled to room temperature over a period of 3-4 hours.
The purified RNA solution was stored at -20.degree. C. until
use.
[0248] Cholesterol was conjugated to siRNA as illustrated in FIG.
1. For the synthesis of these 3'-cholesterol-conjugated siRNAs, an
appropriately modified solid support was used for RNA synthesis.
The modified solid support was prepared as follows:
Diethyl-2-azabutane-1,4-dicarboxylate AA
##STR00001##
[0250] A 4.7 M aqueous solution of sodium hydroxide (50 mL) was
added into a stirred, ice-cooled solution of ethyl glycinate
hydrochloride (32.19 g, 0.23 mole) in water (50 mL). Then, ethyl
acrylate (23.1 g, 0.23 mole) was added and the mixture was stirred
at room temperature until the completion of reaction was
ascertained by TLC (19 h). After 19 h which it was partitioned with
dichloromethane (3.times.100 mL). The organic layer was dried with
anhydrous sodium sulfate, filtered and evaporated. The residue was
distilled to afford AA (28.8 g, 61%).
3-{Ethoxycarbonylmethyl-[6-(9H-fluoren-9-ylmethoxycarbonyl-amino)-hexanoyl-
]-amino}-propionic acid ethyl ester AB
##STR00002##
[0252] Fmoc-6-amino-hexanoic acid (9.12 g, 25.83 mmol) was
dissolved in dichloromethane (50 mL) and cooled with ice.
Diisopropylcarbodiimde (3.25 g, 3.99 mL, 25.83 mmol) was added to
the solution at 0.degree. C. It was then followed by the addition
of Diethyl-azabutane-1,4-dicarboxylate (5 g, 24.6 mmol) and
dimethylamino pyridine (0.305 g, 2.5 mmol). The solution was
brought to room temperature and stirred further for 6 h. the
completion of the reaction was ascertained by TLC. The reaction
mixture was concentrated in vacuum and to the ethylacetate was
added to precipitate diisopropyl urea. The suspension was filtered.
The filtrate was washed with 5% aqueous hydrochloric acid, 5%
sodium bicarbonate and water. The combined organic layer was dried
over sodium sulfate and concentrated to give the crude product
which was purified by column chromatography (50% EtOAC/Hexanes) to
yield 11.87 g (88%) of AB.
3-[(6-Amino-hexanoyl)-ethoxycarbonylmethyl-amino]-propionic acid
ethyl ester AC
##STR00003##
[0254]
3-{Ethoxycarbonylmethyl-[6-(9H-fluoren-9-ylmethoxycarbonylamino)-he-
xanoyl]-amino}-propionic acid ethyl ester AB (11.5 g, 21.3 mmol)
was dissolved in 20% piperidine in dimethylformamide at 0.degree.
C. The solution was continued stirring for 1 h. The reaction
mixture was concentrated in vacuum and the residue water was added
and the product was extracted with ethyl acetate. The crude product
was purified by converting into hydrochloride salt.
3-({6-[17-(1,5-Dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,1-
5,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yloxycarbonylamino]-h-
exanoyl}ethoxycarbonylmethyl-amino)-propionic acid ethyl ester
AD
##STR00004##
[0256] The hydrochloride salt of
3-[(6-Amino-hexanoyl)-ethoxycarbonylmethyl-amino]-propionic acid
ethyl ester AC (4.7 g, 14.8 mmol) was taken up in dichloromethane.
The suspension was cooled to 0.degree. C. on ice. To the suspension
diisopropylethylamine (3.87 g, 5.2 mL, 30 mmol) was added. To the
resulting solution cholesteryl chloroformate (6.675 g, 14.8 mmol)
was added. The reaction mixture was stirred overnight. The reaction
mixture was diluted with dichloromethane and washed with 10%
hydrochloric acid. The product was purified by flash chromatography
(10.3 g, 92%).
1-{6-[17-(1,5-Dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15-
,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yloxycarbonylamino]-he-
xanoyl}-4-oxo-pyrrolidine-3-carboxylic acid ethyl ester AE
##STR00005##
[0258] Potassium t-butoxide (1.1 g, 9.8 mmol) was slurried in 30 mL
of dry toluene. The mixture was cooled to 0.degree. C. on ice and 5
g (6.6 mmol) of diester AD was added slowly with stirring within 20
mins. The temperature was kept below 5.degree. C. during the
addition.
[0259] The stirring was continued for 30 mins at 0.degree. C. and 1
mL of glacial acetic acid was added, immediately followed by 4 g of
NaH.sub.2PO.sub.4.H.sub.2O in 40 mL of water The resultant mixture
was extracted twice with 100 mL of dichloromethane each and the
combined organic extracts were washed twice with 10 mL of phosphate
buffer each, dried, and evaporated to dryness. The residue was
dissolved in 60 mL of toluene, cooled to 0.degree. C. and extracted
with three 50 mL portions of cold pH 9.5 carbonate buffer. The
aqueous extracts were adjusted to pH 3 with phosphoric acid, and
extracted with five 40 mL portions of chloroform which were
combined, dried and evaporated to a residue. The residue was
purified by column chromatography using 25% ethylacetate/hexane to
afford 1.9 g of b-ketoester (39%).
[6-(3-Hydroxy-4-hydroxymethyl-pyrrolidin-1-yl)-6-oxo-hexyl]-carbamic
acid
17-(1,5-dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,1-
7-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl ester AF
##STR00006##
[0261] Methanol (2 mL) was added dropwise over a period of 1 h to a
refluxing mixture of b-ketoester AE (1.5 g, 2.2 mmol) and sodium
borohydride (0.226 g, 6 mmol) in tetrahydrofuran (10 mL). Stirring
was continued at reflux temperature for 1 h. After cooling to room
temperature, 1 N HCl (12.5 mL) was added, the mixture was extracted
with ethylacetate (3.times.40 mL). The combined ethylacetate layer
was dried over anhydrous sodium sulfate and concentrated in vacuum
to yield the product which was purified by column chromatography
(10% MeOH/CHCl.sub.3) (89%).
(6-{3-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-hydroxy-pyrrolidin-1-
-yl}-6-oxo-hexyl)-carbamic acid
17-(1,5-dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,1-
7-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl ester AG
##STR00007##
[0263] Diol AF (1.25 gm 1.994 mmol) was dried by evaporating with
pyridine (2.times.5 mL) in vacuo. Anhydrous pyridine (10 mL) and
4,4'-dimethoxytritylchloride (0.724 g, 2.13 mmol) were added with
stirring. The reaction was carried out at room temperature
overnight. The reaction was quenched by the addition of methanol.
The reaction mixture was concentrated in vacuum and to the residue
dichloromethane (50 mL) was added. The organic layer was washed
with 1M aqueous sodium bicarbonate. The organic layer was dried
over anhydrous sodium sulfate, filtered and concentrated. The
residual pyridine was removed by evaporating with toluene. The
crude product was purified by column chromatography (2%
MeOH/Chloroform, Rf=0.5 in 5% MeOH/CHCl.sub.3) (1.75 g, 95%).
Succinic acid
mono-(4-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-1-{6-[17-(1,5-dimet-
hyl-hexyl)-10,13-dimethyl
2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H
cyclopenta[a]phenanthren-3-yloxycarbonylamino]-hexanoyl}-pyrrolidin-3-yl)-
ester AH
##STR00008##
[0265] Compound AG (1.0 g, 1.05 mmol) was mixed with succinic
anhydride (0.150 g, 1.5 mmol) and DMAP (0.073 g, 0.6 mmol) and
dried in a vacuum at 40.degree. C. overnight. The mixture was
dissolved in anhydrous dichloroethane (3 mL), triethylamine (0.318
g, 0.440 mL, 3.15 mmol) was added and the solution was stirred at
room temperature under argon atmosphere for 16 h. It was then
diluted with dichloromethane (40 mL) and washed with ice cold
aqueous citric acid (5 wt %, 30 mL) and water (2.times.20 mL). The
organic phase was dried over anhydrous sodium sulfate and
concentrated to dryness. The residue was used as such for the next
step.
Cholesterol Derivatised CPG AI
##STR00009##
[0267] Succinate AH (0.254 g, 0.242 mmol) was dissolved in a
mixture of dichloromethane/acetonitrile (3:2, 3 mL). To that
solution DMAP (0.0296 g, 0.242 mmol) in acetonitrile (1.25 mL),
2,2'-Dithio-bis(5-nitropyridine) (0.075 g, 0.242 mmol) in
acetonitrile/dichloroethane (3:1, 1.25 mL) were added successively.
To the resulting solution triphenylphosphine (0.064 g, 0.242 mmol)
in acetonitrile (0.6 ml) was added. The reaction mixture turned
bright orange in color. The solution was agitated briefly using
wrist-action shaker (5 mins). Long chain alkyl amine-CPG (LCAA-CPG)
(1.5 g, 61 mm/g) was added. The suspension was agitated for 2 h.
The CPG was filtered through a sintered funnel and washed with
acetonitrile, dichloromethane and ether successively. Unreacted
amino groups were masked using acetic anhydride/pyridine. The
loading capacity of the CPG was measured by taking UV measurement
(37 mM/g).
[0268] The synthesis and structure of cholesterol conjugated RNA
strands is illustrated in FIG. 1.
Example 2
siRNAs were Designed to Target Regions in Human and Mouse ApoB
Genes
[0269] Nucleic acid sequences are represented below using standard
nomenclature, and specifically the abbreviations of Table 2.
TABLE-US-00002 TABLE 2 Abbreviations of nucleotide monomersused in
nucleic acid sequence representation. It will be understood that
these monomers, when present in an oligonucleotide, are mutually
linked by 5'-3'-phosphodiester bonds. Abbreviation.sup.a
Nucleotide(s) A, a 2'-deoxy-adenosine-5'-phosphate, adenosine-5'-
phosphate C, c 2'-deoxy-cytidine-5'-phosphate,
cytidine-5'-phosphate G, g 2'-deoxy-guanosine-5'-phosphate,
guanosine-5'- phosphate T, t 2'-deoxy-thymidine-5'-phosphate,
thymidine-5'- phosphate U, u 2'-deoxy-uridine-5'-phosphate,
uridine-5'-phosphate Y, y pyrimidine (C or T, c or u) R, r purine
(A or G, a or g) N, n any (G, A, C, or T, g, a, c or u) am
2'-O-methyladenosine-5'-phosphate cm
2'-O-methylcytidine-5'-phosphate gm
2'-O-methylguanosine-5'-phosphate tm
2'-O-methyl-thymidine-5'-phosphate um
2'-O-methyluridine-5'-phosphate af
2'-fluoro-2'-deoxy-adenosine-5'-phosphate cf
2'-fluoro-2'-deoxy-cytidine-5'-phosphate gf
2'-fluoro-2'-deoxy-guanosine-5'-phosphate tf
2'-fluoro-2'-deoxy-thymidine-5'-phosphate uf
2'-fluoro-2'-deoxy-uridine-5'-phosphate A, C, G, T, U, a,
underlined: nucleoside-5'-phosphorothioate c, g, t, u am, cm, gm,
tm, underlined: 2-O-methyl-nucleoside-5'-phosphorothioate um bold
italic: 2'-deoxy-adenosine, 2'-deoxy-cytidine, 2'-deoxy-guanosine,
2'-deoxy-thymidine, 2'-deoxy- uridine, adenosine, cytidine,
guanosine, thymidine, uridine (5'-hydroxyl) bold italic:
2'-O-methyl-adenosine, 2'-O-methyl- cytidine,
2'-O-methyl-guanosine, 2'-O-methyl- thymidine, 2'-O-methyl-uridine
(5'-hydroxyl) .sup.acapital letters represent
2'-deoxyribonucleotides (DNA), lower case letters represent
ribonucleotides (RNA)
[0270] Certain oligonucleotides described herein were modified to
include a cholesterol moiety linked to their 3'-end (see FIG. 1).
These are denoted as 5'-(n).sub.n(Chol)-3'.
[0271] Where this text refers to "position n" (n being an integer
number) within a given nucleotide sequence, this is meant to refer
to the n-th nucleotide in the nucleotide sequence, wherein the
5'-most nucleotide is counted as the first nucleotide, and counting
is continued in the 3'-direction.
[0272] Since therapeutics for use in humans are typically first
tested in animals, we designed siRNAs that would potentially have
an effect both in an animal model system as well as in a human. The
animal model system chosen was the mouse, mus musculus. Therefore,
the first criterion in choosing sequences for siRNA targeting was
cross-reactivity between mouse and human ApoB.
[0273] In order to select siRNAs that would potentially inhibit
ApoB gene expression in mouse as well as in humans, the sequences
coding for the open reading frame of mouse (GenBank Accession
number: XM.sub.--137955) and human (GenBank Accession number:
NM.sub.--000384) ApoB were aligned using a pair wise BLAST
algorithm. The mathematical algorithm used in BLAST programs is
described in Altschul et al. (Nucleic Acids Res. 25:3389-3402,
1997). Regions with identity in 23 or more consecutive nucleotides
(nucleotides in mouse open reading frame: 463-494, 622-647,
658-680, 701-725, 1216-1240, 1282-1320, 1299-1328, 1339-1362,
2124-2155, 2807-2830, 2809-2837, 2860-2901, 3035-3057, 3103-3125,
3444-3467, 3608-3635, 4130-4167, 4374-4402, 4503-4525, 5962-5985,
6696-6724, 9232-9257, 9349-9372, 10177-10213, 10477-10505,
10791-10814, 11020-11045, 12227-12251, 13539-13572) were
identified.
[0274] All possible nucleotide sequences of 23 nucleotides in
length were determined. This set represented 170 potential siRNA
targeting regions. These sequences were compared by BLAST searching
(word size 7, mismatch penalty -1, expect value 1000) against human
and mouse genome and mRNA databases. All potential 23 nucleotide
target regions with 3 or less sequence mismatches to any non-ApoB
sequence in the mouse mRNA and mouse genome databases were excluded
from the initial set. The remaining 84 potential targeting regions
served as template to derive the siRNA sense and antisense strands.
The sense strand of each siRNA was identical to nucleotides 3 to 23
(5' to 3') from the potential target region. The antisense strand
was defined as the reverse complement of the full 23 nucleotide
target region. The resulting siRNAs had 2 nucleotide overhangs at
the 3'-end of the antisense strand and a base-paired region of 21
nucleotides. 81 of these 84 potential siRNAs were synthesized and
their efficacy in inhibiting the expression of ApoB in cultured
human HepG2 cells was determined. For those siRNAs effecting a
repression of ApoB mRNA expression to less than 50% of ApoB mRNA
levels in untreated control cells, the stability in human and/or
mouse serum was also determined.
[0275] The sequences of the sense and antisense strands of the 84
synthesized siRNA duplexes are shown in Table 3. Sense strands
represent nucleotides 3-23 of all 23 nucleotide regions which are:
(a) homologous between the open reading frames (ORF) of mouse
(GenBank Accession number: XM.sub.--137955) and human (GenBank
Accession number: NM.sub.--000384) ApoB; and (b) were found to have
4 or more mismatches when compared to all other entries in the
human and mouse genome and mRNA databases. The antisense strands
shown in Table 3 are complementary to nucleotides 1-23 of the 23
sense strand nucleotide regions. The position of the 5'-most
nucleotide of the corresponding 23 nucleotide region in the ORF of
mouse ApoB is also given.
TABLE-US-00003 TABLE 3 Nucleic acid sequences of unmodified siRNA
duplexes SEQ. SEQ. ID ID Sequence antisense Duplex Start No.
Sequence sense strand No. strand descriptor.sup.a pos..sup.b 1
agccuugguucaguguggac 2 uccacacugaaccaaggcuugu AL-DUP 5000 1302 3
gaacaccaacuucuuccacg 4 guggaagaaguugguguucauc AL-DUP 5001 2865 5
auugauugaccuguccauuc 6 aauggacaggucaaucaaucuu AL-DUP 5002 13539 7
auggacucaucugcuacagc 8 cuguagcagaugaguccauuug AL-DUP 5003 3610 9
uugaccuguccauucaaaac 10 uuuugaauggacaggucaauca AL-DUP 5004 13544 11
uugugacaaauaugggcauc 12 augcccauauuugucacaaacu AL-DUP 5005 2810 13
uugguucaguguggacagcc 14 gcuguccacacugaaccaaggc AL-DUP 5006 1306 15
ggacucaucugcuacagcuu 16 agcuguagcagaugaguccauu AL-DUP 5007 3612 17
uugauugaccuguccauuca 18 gaauggacaggucaaucaaucu AL-DUP 5008 13540 19
ugauugaccuguccauucaa 20 ugaauggacaggucaaucaauc AL-DUP 5009 13541 21
aaauggacucaucugcuaca 22 guagcagaugaguccauuugga AL-DUP 5010 3608 23
auugaccuguccauucaaaa 24 uuugaauggacaggucaaucaa AL-DUP 5011 13543 25
gauugaccuguccauucaaa 26 uugaauggacaggucaaucaau AL-DUP 5012 13542 27
guguauggcuucaacccuga 28 caggguugaagccauacaccuc AL-DUP 5013 466 29
cugugggauuccaucugcca 30 ggcagauggaaucccacagacu AL-DUP 5014 4136 31
gacuuccugaauaacuaugc 32 cauaguuauucaggaagucuau AL-DUP 5015 9349 33
caauuugaucaguauauuaa 34 uaauauacugaucaaauuguau AL-DUP 5016 6697 35
gacucaucugcuacagcuua 36 aagcuguagcagaugaguccau AL-DUP 5017 3613 37
uacuccaacgccagcuccac 38 uggagcuggcguuggaguaagc AL-DUP 5018 3103 39
ugacaaauaugggcaucauc 40 augaugcccauauuugucacaa AL-DUP 5019 2813 41
uguauggcuucaacccugag 42 ucaggguugaagccauacaccu AL-DUP 5020 467 43
accguguauggaaacugcuc 44 agcaguuuccauacacgguauc AL-DUP 5021 703 45
auaccguguauggaaacugc 46 caguuuccauacacgguaucca AL-DUP 5022 701 47
aaucaagugucaucacacug 48 agugugaugacacuugauuuaa AL-DUP 5023 10178 49
gguguauggcuucaacccug 50 aggguugaagccauacaccucu AL-DUP 5024 465 51
uuugugacaaauaugggcau 52 ugcccauauuugucacaaacuc AL-DUP 5025 2809 53
uaccguguauggaaacugcu 54 gcaguuuccauacacgguaucc AL-DUP 5026 702 55
aaaucaagugucaucacacu 56 gugugaugacacuugauuuaaa AL-DUP 5027 10177 57
agguguauggcuucaacccu 58 ggguugaagccauacaccucuu AL-DUP 5028 464 59
ggcuucaacccugagggcaa 60 ugcccucaggguugaagccaua AL-DUP 5029 472 61
aacaccaacuucuuccacga 62 cguggaagaaguugguguucau AL-DUP 5030 2866 63
uauggcuucaacccugaggg 64 ccucaggguugaagccauacac AL-DUP 5031 469 65
uggcuucaacccugagggca 66 gcccucaggguugaagccauac AL-DUP 5032 471 67
acaccaacuucuuccacgag 68 ucguggaagaaguugguguuca AL-DUP 5033 2867 69
caccaacuucuuccacgagu 70 cucguggaagaaguugguguuc AL-DUP 5034 2868 71
accaacuucuuccacgaguc 72 acucguggaagaaguugguguu AL-DUP 5035 2869 73
augaacaccaacuucuucca 74 ggaagaaguugguguucaucug AL-DUP 5036 2863 75
ugaacaccaacuucuuccac 76 uggaagaaguugguguucaucu AL-DUP 5037 2864 77
gaugaacaccaacuucuucc 78 gaagaaguugguguucaucugg AL-DUP 5038 2862 79
uuccaucugccaucucgaga 80 cucgagauggcagauggaaucc AL-DUP 5039 4144 81
uccaucugccaucucgagag 82 ucucgagauggcagauggaauc AL-DUP 5040 4145 83
caagccuugguucagugugg 84 cacacugaaccaaggcuuguaa AL-DUP 5041 1300 85
ucaagucugugggauuccau 86 uggaaucccacagacuugaggu AL-DUP 5042 4130 87
aucaagugucaucacacuga 88 cagugugaugacacuugauuua AL-DUP 5043 10179 89
auggcuucaacccugagggc 90 cccucaggguugaagccauaca AL-DUP 5044 470 91
ugaccuguccauucaaaacu 92 guuuugaauggacaggucaauc AL-DUP 5045 13545 93
ucaagugucaucacacugaa 94 ucagugugaugacacuugauuu AL-DUP 5046 10180 95
caagugucaucacacugaau 96 uucagugugaugacacuugauu AL-DUP 5047 10181 97
ucaucacacugaauaccaau 98 uugguauucagugugaugacac AL-DUP 5048 10187 99
uguccauucaaaacuaccac 100 ugguaguuuugaauggacaggu AL-DUP 5049 13550
101 cuguccauucaaaacuacca 102 gguaguuuugaauggacagguc AL-DUP 5050
13549 103 ucacacugaauaccaaugcu 104 gcauugguauucagugugauga AL-DUP
5051 10190 105 ccuguccauucaaaacuacc 106 guaguuuugaauggacagguca
AL-DUP 5052 13548 107 accuguccauucaaaacuac 108
uaguuuugaauggacaggucaa AL-DUP 5053 13547 109 aucacacugaauaccaaugc
110 cauugguauucagugugaugac AL-DUP 5054 10189 111
acaagccuugguucagugug 112 acacugaaccaaggcuuguaaa AL-DUP 5055 1299
113 guauggcuucaacccugagg 114 cucaggguugaagccauacacc AL-DUP 5056 468
115 gaccuguccauucaaaacua 116 aguuuugaauggacaggucaau AL-DUP 5057
13546 117 caucacacugaauaccaaug 118 auugguauucagugugaugaca AL-DUP
5058 10188 119 ugugacaaauaugggcauca 120 gaugcccauauuugucacaaac
AL-DUP 5059 2811 121 aagugucaucacacugaaua 122
auucagugugaugacacuugau AL-DUP 5060 10182 123 aacacuaagaaccagaagau
124 ucuucugguucuuaguguuagc AL-DUP 5061 11020 125
aauuugaucaguauauuaaa 126 uuaauauacuguacaaauugua AL-DUP 5062 6698
127 ugaacaucaagaggggcauc 128 augccccucuugauguucagga AL-DUP 5084 623
129 gaacaucaagaggggcauca 130 gaugccccucuugauguucagg AL-DUP 5085 624
131 uccagccccaucacuuuaca 132 guaaagugauggggcuggacac AL-DUP 5086
1282 133 agccccaucacuuuacaagc 134 cuuguaaagugauggggcugga AL-DUP
5087 1285 135 gccccaucacuuuacaagcc 136 gcuuguaaagugauggggcugg
AL-DUP 5088 1286 137 aguuugugacaaauaugggc 138
cccauauuugucacaaacucca AL-DUP 5089 2807 139 gggaaucuuauauuugaucc
140 gaucaaauauaagauucccuuc AL-DUP 5090 2131 141
uacugagcugagaggccuca 142 gaggccucucagcucaguaacc AL-DUP 5091 1218
143 uugggaagaagaggcagcuu 144 agcugccucuucuucccaauua AL-DUP 5092
12228 145 cacauccuccaguggcugaa 146 ucagccacuggaggaugugagu AL-DUP
5093 1339 147 ccccaucacuuuacaagccu 148 ggcuuguaaagugauggggcug
AL-DUP 5094 1287 149 cagccccaucacuuuacaag 150
uuguaaagugauggggcuggac AL-DUP 5095 1284 151 agggaaucuuauauuugauc
152 aucaaauauaagauucccuucu AL-DUP 5096 2130 153
uuuacaagccuugguucagu 154 cugaaccaaggcuuguaaagug AL-DUP 5097 1296
155 gaaucuuauauuugauccaa 156 uggaucaaauauaagauucccu AL-DUP 5098
2133 157 aagggaaucuuauauuugau 158 ucaaauauaagauucccuucua AL-DUP
5099 2129 159 aauagaagggaaucuuauau 160 uauaagauucccuucuauuuug
AL-DUP 5100 2124 161 agaagggaaucuuauauuug 162
aaauauaagauucccuucuauu AL-DUP 5101 2127 163 gacuuccugaauaacuaugca
164 ugcauaguuauucaggaagucua 9350 165 gcaaggaucuggagaaacaac 166
guuguuucuccagauccuugcac 4375 167 caaggaucuggagaaacaaca 168
uguuguuucuccagauccuugca 4376 .sup.aDescriptor refers to annealed
duplex siRNA .sup.bPosition of the 5'-most nucleotide of th e
corresponding 23 nucleotide region in the OFR of mouse ApoB
[0276] Alternatively, for the same set of 84 potential target
regions, siRNAs may be generated with 19 basepairs and 2 nucleotide
dTdT overhangs. The sense strand is then identical to nucleotides 1
to 19, 2 to 20, 3 to 21, 4 to 22, or 5 to 23 from the target
region, and two dT nucleotides are added to the 3''-end of the
oligonucleotide. The reverse complement of the sense strand so
selected would then serve as template for the antisense strand, and
two dT nucleotides would be added to the 3''-end.
Example 3
siRNAs Inhibited ApoB Expression Both on the mRNA as Well as the
Protein Level, in Cell Culture
[0277] The activity of the siRNAs described above was tested in
HepG2 cells.
[0278] HepG2 cells in culture were used for quantitation of ApoB
mRNA in total mRNA isolated from cells incubated with ApoB-specific
siRNAs by branched DNA assay, and of ApoB 100 protein in
supernatant of cells incubated with ApoB-specific siRNAs by
Enzyme-linked immunosorbent assay (ELISA). HepG2 cells were
obtained from American Type Culture Collection (Rockville, Md.,
cat. No. HB-8065) and cultured in MEM (Gibco Invitrogen, Invitrogen
GmbH, Karlsruhe, Germany, cat. No. 21090-022) supplemented to
contain 10% fetal calf serum (FCS) (Biochrom AG, Berlin, Germany,
cat. No. S0115), 2 mM L-Glutamin (Biochrom AG, Berlin, Germany,
cat. No. K0238), Penicillin 100 U/ml, Streptomycin 100 .mu.g/ml
(Biochrom AG, Berlin, Germany, cat. No. A2213), 1.times.
non-essential amino acids (NEA) (Biochrom AG, Berlin, Germany, cat.
No. K0293) and 1 mM sodium pyruvate (Biochrom AG, Berlin, Germany,
cat. No. L0473) at 37.degree. C. in an atmosphere with 5% CO.sub.2
in a humidified incubator (Heraeus HERAcell, Kendro Laboratory
Products, Langenselbold, Germany).
[0279] For transfection with siRNA, HepG2 cells were seeded at a
density of 1.5.times.10.sup.4 cells/well in 96-well plates and
cultured for 24 hours. Transfection of siRNA was carried out with
oligofectamine (Invitrogen GmbH, Karlsruhe, Germany, cat. No.
12252-011) as described by the manufacturer. SiRNAs were
transfected at a concentration of 100 nM for the screening of siRNA
duplexes, and 100, 33, 11, 3.7, 1.2, 0.4, 0.14, and 0.05 nM when
assessing dose response/inhibitor concentration at 50% maximal
inhibition (IC.sub.50). 24 hours after transfection, the medium was
changed and cells were incubated for an additional 24 hours. For
the assessment of ApoB100 protein concentration by enzyme-linked
immunosorbent assay, as described below, supernatant was collected
and stored at -80.degree. C. until analysis. For measurement of
ApoB mRNA by branched DNA assay, as described below, cells were
harvested and lysed following procedures recommended by the
manufacturer of the Quantigene Explore Kit (Genospectra, Fremont,
Calif., USA, cat. No. QG-000-02) for bDNA quantitation of mRNA,
except that 2 .mu.l of a 50 .mu.g/.mu.l stock solution of
Proteinase K (Epicentre, Madison, Wis., USA, Cat. No. MPRK092) was
added to 600 .mu.l of Tissue and Cell Lysis Solution (Epicentre,
Madison, Wis., USA, cat. No. MTC096H). Lysates were stored at
-80.degree. C. until analysis by branched DNA assay.
[0280] NmuLi cells in culture were used for quantitation of murine
ApoB mRNA by branched DNA assay (bDNA assay). NmuLi cells (normal
murine liver, ATCC Number: CRL-1638) were cultured in DMEM
(Biochrom AG, Berlin, Germany, cat. No. F0435) supplemented to
contain 10% fetal calf serum (FCS) (Biochrom AG, Berlin, Germany,
cat. No. 50115) and 2 mM L-Glutamin (Biochrom AG, Berlin, Germany,
cat. No. K0238) at 37.degree. C. under an atmosphere containing 5%
CO.sub.2 in a humidified incubator (Heraeus HERAcell, Kendro
Laboratory Products, Langenselbold, Germany).
[0281] One day before transfection, 4.times.10.sup.3 cells per well
were seeded on 96-well plates. Cells were transfected with siRNAs
in triplicate with oligofectamine according to the manufacturer's
protocol (Invitrogen GmbH, Karlsruhe, Germany, cat. No. 12252-011).
Concentration of the siRNA in the medium during transfection was
200 nM for the screening of 15 unmodified or modified siRNA
duplexes. Following transfection, cells were cultured for 24 h,
after which the growth medium was exchanged for fresh medium not
containing the siRNA. Cell lysates were obtained and stored as
described above for HepG2 cells.
[0282] The sequences of an siRNA duplex used as a non-cholesterol
conjugated control is shown below:
TABLE-US-00004 AL-DUP HCV SEQ. ID No. 169 Sense: 5'-
cggcuagcugugaaaggucc-3' SEQ. ID No. 170 Antisense: 5'-
gaccuuucacagcuagccguga-3'
[0283] The sense strand of AL-DUP HCV corresponds to positions
9472-9493 of the 3'-untranslated region of hepatitis C virus
(Accession number: D89815).
[0284] The sequences of an siRNA duplex used as a
cholesterol-conjugated control is shown below:
TABLE-US-00005 AL-DUP 5129 SEQ. ID No. 171 Sense:
5'-ccacaugaagcagcacgacuu(Chol)-3' SEQ. ID No. 172 Antisense:
5'-aagucgugcugcuucaugug-3'
[0285] Nucleotides 1-21 of the sense strand correspond to positions
843-864 in cloning vector pEGFP-C3 with enhanced green fluorescent
protein (GenBank Accession number: U57607).
[0286] ApoB100 protein levels in cell supernatants were measured by
ELISA assay. Clear Flat Bottom Polystyrene High Bind Microplates
(Corning B.V. Life Sciences, Schiphol-Rijk, The Netherlands, cat.
no. 9018) were used for the assays. Polyclonal antibody goat
anti-human-apolipoprotein B (Chemicon International GmbH, Hofheim,
Germany, cat. no. AB742) was diluted 1:1000 in phosphate buffered
saline (PBS) (PBS Dulbecco w/o Ca.sup.2+, Mg.sup.2+, Biochrom AG,
Berlin, Germany, cat. No. L182-05) and 100 .mu.l of this dilution
was coated on 96-well plates at 4.degree. C. overnight. After
blocking with 300 .mu.l of 1% bovine serum albumin (BSA) (Carl Roth
GmbH & Co KG, Karlsruhe, Germany, cat. no. 8076.2) in PBS the
plate was washed three times with PBS.
[0287] Cell culture supernatant was thawed and diluted 1:1 with PBS
containing 0.1% Tween 20 (Carl Roth GmbH & Co KG, Karlsruhe,
Germany, cat. No. 9127.1) and 0.1% BSA. 100 .mu.l of this dilution
was added to each well. After an incubation time of 2 hours at room
temperature, the plate was washed five times with PBS containing
0.1% Tween 20 followed by three washes with PBS. 100 .mu.l of a
horseradish-peroxidase conjugated Goat Anti-Human Apolipoprotein
B-100 polyclonal antibody (Academy Bio-Medical Company, Houston,
Tex., USA, cat. No. 20H-G1-b) diluted 1:1000 in PBS containing 0.1%
Tween 20 and 3% BSA was added to each well. The plate was incubated
for 2 hours at room temperature. After washing the plate five times
with PBS containing 0.1% Tween 20 and three times with PBS, wells
were incubated with 0.9 mg/ml OPD (o-phenylendiamine
dihydrochloride, Merck Biosciences GmbH, Bad Soden, Germany cat.
No. 523121) in 24 mmol/L citric acid buffer (Sigma-Aldrich,
Taufkirchen, Germany, cat. no. C1909-1KG), pH 5.0, containing 0.03%
hydrogen peroxide (Merck Biosciences GmbH, Bad Soden, Germany cat.
No. 386790). The enzyme reaction was halted by adding 0.5 mol/L
H.sub.2SO.sub.4 (Merck KgaA, Darmstadt, Germany, cat. No. 100731)
and absorbance at 490 nm was measured on a spectrophotometer
(Perkin Elmer Wallac Victor3 1420 multilabel reader, PerkinElmer
LAS GmbH, Rodgau, Germany). siRNA duplexes unrelated to any mouse
gene were used as control, and the activity of a given ApoB
specific siRNA duplex was expressed as percent ApoB protein
concentration in the supernatant of treated cells relative to ApoB
protein concentration in the supernatant of cells treated with the
control siRNA duplex. The conjugation of a cholesterol moiety to
the sense strand of siRNA duplexes enhanced the ApoB
secretion-inducing effect in cultured HepG2 cells. Therefore, one
siRNA duplex control included a conjugated cholesterol moiety
(AL-DUP 5129).
[0288] ApoB100 mRNA levels were measured by branched-DNA (bDNA)
assay. The assay was performed using the Quantigene Explore Kit
(Genospectra, Fremont, Calif., USA, cat. No. QG-000-02). Frozen
lysates were thawed at room temperature, and ApoB and GAPDH mRNA
quantified using the Quantigene Explore Kit according to
manufacturer's instructions. Nucleic acid sequences for Capture
Extender (CE), Label Extender (LE) and blocking (BL) probes were
selected from the nucleic acid sequences of ApoB and GAPDH with the
help of the QuantiGene ProbeDesigner Software 2.0 (Genospectra,
Fremont, Calif., USA, cat. No. QG-002-02). Probe nucleotide
sequences used in quantization of murine and human ApoB are shown
in Table 4 and Table 5, respectively. Probe nucleotide sequences
used in quantization of murine and human GAPDH are shown in Table 6
and Table 7, respectively.
TABLE-US-00006 TABLE 4 DNA probes for murine ApoB used in
branched-DNA assays SEQ. ID. Probe type.sup.a Nucleotide sequence
No. CE TCATTCTCCAGCAGCAGGGTTTTTCTCTTGGAAAGAAAGT 173 CE
AAGCGGCCGTTTGTTGATATTTTTCTCTTGGAAAGAAAGT 174 CE
TTTTTGCTGTCTGCACCCATTTTTCTCTTGGAAAGAAAGT 175 CE
AAATATTGTCCATTTTTGAGAAGAAGTTTTTCTCTTGGAAAGAAAGT 176 CE
ATTCAGCTTCAGTGGCTCCATTTTTCTCTTGGAAAGAAAGT 177 CE
ATGTCTGCATTTAGCCTATGGCTTTTTTCTCTTGGAAAGAAAGT 178 LE
GCCCAAGCTCTGCATTCAATTTTTAGGCATAGGACCCGTGTCT 179 LE
TTTCATGGATGCCCCAGAGTTTTTAGGCATAGGACCCGTGTCT 180 LE
CTGAATTTTGCATGGTGTTCTTTTTTTTAGGCATAGGACCCGTGTCT 181 LE
GGCAGCTCTCCCATCAAGTTTTTAGGCATAGGACCCGTGTCT 182 LE
AATCATGGCCTGGTAAATGCTTTTTAGGCATAGGACCCGTGTCT 183 LE
AGCATAGGAGCCCATCAAATCATTTTTTAGGCATAGGACCCGTGTCT 184 LE
ACTGTGTGTGTGGTCAAGTTTCATCTTTTTTAGGCATAGGACCCGTGTCT 185 LE
TAGGGCTGTAGCTGTAAGTTAAAATTTTTTAGGCATAGGACCCGTGTCT 186 LE
TCAAATCTAGAGCACCATATCTCAGTTTTTAGGCATAGGACCCGTGTCT 187 LE
CCGAAACCTTCCATTGTTGTTTTTAGGCATAGGACCCGTGTCT 188 LE
GATATGTTTCAGCTCATTATTTTGATAGTTTTTAGGCATAGGACCCGTGTCT 189 LE
TACTACCAGGTCAGTATAAGATATGGTATTTTTTAGGCATAGGACCCGTGTCT 190 LE
AATTCGACACCCTGAACCTTAGTTTTTAGGCATAGGACCCGTGTCT 191 BL
CCCCAGTGACACCTCTGTGA 192 BL CGGCTGAGTTTGAAGTTGAAGAT 193 BL
GGACAGCCTCAGCCCTTC 194 BL CCAGTGAGAGACCTGCAATGTTCA 195 BL
CTGCTTATAGAACTTGTCTCCACTG 196 BL TCGTTGCTTAAAGTAGTTATGAAAGA 197 BL
TTCCTTTAAAGTTGCCACCCA 198 BL CACAGTGTCTGCTCTGTAACTTG 199 .sup.aCE =
Capture Extender probe; LE = Label Extender probe; BL = blocking
probe
TABLE-US-00007 TABLE 5 DNA probes for human ApoB used in
branched-DNA assays Probe type.sup.a Nucleotide sequence SEQ. ID.
No. CE ATTGGATTTTCAGAATACTGTATAGCTTTTTTCTCTTGGAAAGAAAGT 200 CE
CTGCTTCGTTTGCTGAGGTTTTTTCTCTTGGAAAGAAAGT 201 CE
CAGTGATGGAAGCTGCGATATTTTTCTCTTGGAAAGAAAGT 202 CE
AACTTCTAATTTGGACTCTCCTTTGTTTTTCTCTTGGAAAGAAAGT 203 CE
CTCCTTCAGAGCCAGCGGTTTTTCTCTTGGAAAGAAAGT 204 CE
CTCCCATGCTCCGTTCTCATTTTTCTCTTGGAAAGAAAGT 205 CE
GGGTAAGCTGATTGTTTATCTTGATTTTTCTCTTGGAAAGAAAGT 206 LE
GTTCCATTCCCTATGTCAGCATTTTTAGGCATAGGACCCGTGTCT 207 LE
TTAATCTTAGGGTTTGAGAGTTGTGTTTTTAGGCATAGGACCCGTGTCT 208 LE
ACTGTGTTTGATTTTCCCTCAATATTTTTAGGCATAGGACCCGTGTCT 209 LE
GTATTTTTTTCTGTGTGTAAACTTGCTTTTTAGGCATAGGACCCGTGTCT 210 LE
AATCACTCCATTACTAAGCTCCAGTTTTTAGGCATAGGACCCGTGTCT 211 BL
GCCAAAAGTAGGTACTTCAATTG 212 BL TTGCATCTAATGTGAAAAGAGGA 213 BL
ATTTGCTTGAAAATCAAAATTGA 214 BL GTACTTGCTGGAGAACTTCACTG 215 BL
CATTTCCAAAAAACAGCATTTC 216 .sup.aCE = Capture Extender probe; LE =
Label Extender probe; BL = blocking probe
TABLE-US-00008 TABLE 6 DNA probes for murine GAPDH used in
branched-DNA assays Probe type.sup.a Nucleotide sequence SEQ. ID.
No. CE AAATGGCAGCCCTGGTGATTTTTCTCTTGGAAAGAAAGT 217 CE
CTTGACTGTGCCGTTGAATTTTTTTTCTCTTGGAAAGAAAGT 218 CE
TCTCGCTCCTGGAAGATGGTTTTTCTCTTGGAAAGAAAGT 219 CE
CCGGCCTTCTCCATGGTTTTTTCTCTTGGAAAGAAAGT 220 LE
ACAATCTCCACTTTGCCACTGTTTTTAGGCATAGGACCCGTGTCT 221 LE
ATGTAGACCATGTAGTTGAGGTCAATTTTTAGGCATAGGACCCGTGTCT 222 LE
ACAAGCTTCCCATTCTCGGTTTTTAGGCATAGGACCCGTGTCT 223 LE
GATGGGCTTCCCGTTGATTTTTTAGGCATAGGACCCGTGTCT 224 LE
ACATACTCAGCACCGGCCTTTTTTAGGCATAGGACCCGTGTCT 225 BL
GAAGGGGTCGTTGATGGC 226 BL CGTGAGTGGAGTCATACTGGAA 227 BL
ACCCCATTTGATGTTAGTGGG 228 BL GTGAAGACACCAGTAGACTCCAC 229 .sup.aCE =
Capture Extender probe; LE = Label Extender probe; BL = blocking
probe
TABLE-US-00009 TABLE 7 DNA probes for human GAPDH used in
branched-DNA assays Probe type.sup.a Nucleotide sequence SEQ. ID.
No. CE AATTTGCCATGGGTGGAATTTTTTCTCTTGGAAAGAAAGT 230 CE
GAGGGATCTCGCTCCTGGATTTTTCTCTTGGAAAGAAAGT 231 CE
CCCAGCCTTCTCCATGGTTTTTTCTCTTGGAAAGAAAGT 232 CE
CTCCCCCCTGCAAATGAGTTTTTCTCTTGGAAAGAAAGT 233 LE
GCCTTGACGGTGCCATGTTTTTAGGCATAGGACCCGTGTCT 234 LE
ATGACAAGCTTCCCGTTCTCTTTTTAGGCATAGGACCCGTGTCT 235 LE
GATGGTGATGGGATTTCCATTTTTTTAGGCATAGGACCCGTGTCT 236 LE
CATCGCCCCACTTGATTTTTTTTTAGGCATAGGACCCGTGTCT 237 LE
ACGACGTACTCAGCGCCATTTTTAGGCATAGGACCCGTGTCT 238 LE
GCAGAGATGATGACCCTTTTGTTTTTAGGCATAGGACCCGTGTCT 239 BL
GTGAAGACGCCAGTGGACTC 240 .sup.aCE = Capture Extender probe; LE =
Label Extender probe; BL = blocking probe
[0289] The ApoB mRNA levels were normalized across different
samples by comparing the ratio of ApoB mRNA to GAPDH mRNA present
in the samples. AL-DUP HCV, which does not target any mouse gene,
and the cholesterol conjugated AL-DUP 5129 were used as controls.
The activity of a given ApoB specific siRNA duplex was expressed as
a percentage of ApoB mRNA (ApoB mRNA/GAPDH mRNA) in treated cells
relative to cells treated with the control siRNA.
[0290] Table 8 shows the results from screening 81 siRNA duplexes
for their activity in reducing ApoB mRNA levels in HepG2 cell
cultures and ApoB protein levels in the supernatant of NmuLi cell
cultures.
TABLE-US-00010 TABLE 8 Percentage ApoB mRNA and protein following
treatment with siRNA (ApoB mRNA/GAPDH ApoB protein in HepG2 mRNA)
in HEPG2 cultured cell culture supernatant Duplex descriptor cells
relative to controls relative to controls AL-DUP 5000 204 35 AL-DUP
5001 141 37 AL-DUP 5002 68 29 AL-DUP 5003 121 119 AL-DUP 5004 55 55
AL-DUP 5005 250 129 AL-DUP 5006 174 99 AL-DUP 5007 96 72 AL-DUP
5008 93 67 AL-DUP 5009 68 92 AL-DUP 5010 79 41 AL-DUP 5011 98 44
AL-DUP 5012 111 40 AL-DUP 5013 37 24 AL-DUP 5014 112 43 AL-DUP 5015
165 54 AL-DUP 5016 108 44 AL-DUP 5017 117 46 AL-DUP 5018 414 93
AL-DUP 5019 46 56 AL-DUP 5020 43 43 AL-DUP 5021 103 45 AL-DUP 5022
86 26 AL-DUP 5023 218 74 AL-DUP 5024 25 19 AL-DUP 5025 64 47 AL-DUP
5026 84 70 AL-DUP 5027 45 51 AL-DUP 5028 41 31 AL-DUP 5029 44 29
AL-DUP 5030 49 27 AL-DUP 5031 45 36 AL-DUP 5032 82 47 AL-DUP 5033
115 87 AL-DUP 5034 58 38 AL-DUP 5035 46 26 AL-DUP 5036 47 24 AL-DUP
5037 120 53 AL-DUP 5038 62 33 AL-DUP 5039 56 45 AL-DUP 5040 78 70
AL-DUP 5041 387 45 AL-DUP 5042 232 52 AL-DUP 5043 65 54 AL-DUP 5044
95 55 AL-DUP 5045 65 57 AL-DUP 5046 28 37 AL-DUP 5047 29 56 AL-DUP
5048 28 16 AL-DUP 5049 31 36 AL-DUP 5050 55 54 AL-DUP 5051 65 55
AL-DUP 5052 49 49 AL-DUP 5053 37 46 AL-DUP 5054 54 43 AL-DUP 5055
205 101 AL-DUP 5056 67 72 AL-DUP 5057 77 66 AL-DUP 5058 85 37
AL-DUP 5059 116 61 AL-DUP 5060 45 35 AL-DUP 5061 40 43 AL-DUP 5062
63 47 AL-DUP 5084 26 52 AL-DUP 5085 35 57 AL-DUP 5086 36 69 AL-DUP
5087 71 27 AL-DUP 5088 35 28 AL-DUP 5089 26 33 AL-DUP 5090 64 51
AL-DUP 5091 76 90 AL-DUP 5092 37 81 AL-DUP 5093 21 64 AL-DUP 5094
15 29 AL-DUP 5095 54 57 AL-DUP 5096 55 62 AL-DUP 5097 8 29 AL-DUP
5098 11 24 AL-DUP 5099 43 48 AL-DUP 5100 17 57 AL-DUP 5101 15
39
[0291] The 27 most active siRNA duplexes of Table 8 were determined
to be those with a residual ApoB mRNA/GAPDH mRNA <31% of
controls or residual ApoB protein levels <35% of controls. These
siRNA duplexes were chosen for further analysis and establishment
of 1050 values. These were: AL-DUP 5000, AL-DUP 5002, AL-DUP 5013,
AL-DUP 5022, AL-DUP 5024, AL-DUP 5028, AL-DUP 5029, AL-DUP 5030,
AL-DUP 5035, AL-DUP 5036, AL-DUP 5038, AL-DUP 5046, AL-DUP 5047,
AL-DUP 5048, AL-DUP 5049, AL-DUP 5060, AL-DUP 5083, AL-DUP 5084,
AL-DUP 5087, AL-DUP 5088, AL-DUP 5089, AL-DUP 5093, AL-DUP 5094,
AL-DUP 5097, AL-DUP 5098, AL-DUP 5100, AL-DUP 5101.
[0292] Dose escalation studies were performed using the
above-mentioned 27 siRNA duplexes, where ApoB mRNA was quantified
in NmuLi cells and ApoB protein was quantified in cell culture
supernatant of HepG2 cells after incubation with 100, 33, 11, 3.7,
1.2, 0.4, 0.14, or 0.05 nM solutions of the respective siRNA
duplex. The minimum residual ApoB mRNA and ApoB protein levels were
determined. For those 15 of the above 27 siRNA showing the lowest
combined minimum residual ApoB mRNA and protein levels, the dose
escalation was repeated three times, the resulting data were used
to calculate inhibitor concentration at 50% maximal inhibition
(IC50), and an average value was computed over the three
determinations. IC50 was calculated by applying the data from the
dose escalation experiments to curve fitting routines implemented
in the computer software Xlfit 4 (ID Business Solutions Ltd.,
Guildford, UK). IC50 values were computed using the parameterized
equations obtained from the line fit using the following
parameters: Dose Response One Site, 4 Parameter Logistic Model,
fit=(A+((B-A)/(1+(((10 C)/x) D)))), inv=((10 C)/((((B-A)/(y-A))-1)
(1/D))), res=(y-fit) (by way of example, see FIG. 2).
[0293] Table 9 shows the average IC50 values for the five ApoB
siRNAs that reduced both mRNA and protein levels by >70% in
NmuLi cells. Control experiments measured minimal residual ApoB
mRNA/GAPDH mRNA in cultured NmuLi cells in percentage of untreated
controls, and minimal residual ApoB protein in HepG2 cell
supernatant in percentage of untested controls
TABLE-US-00011 TABLE 9 IC50 of selected siRNAs Minimum Minimum
residual residual IC.sub.50 ApoB mRNA/ ApoB protein in Duplex (ApoB
protein GAPDH mRNA cell supernatant denominator concentration) in %
of controls in % of controls AL-DUP 5097 0.3 nM 15% 18% AL-DUP 5098
0.7 nM 9% 20% AL-DUP 5094 0.7 nM 14% 7% AL-DUP 5048 0.9 nM 11% 6%
AL-DUP 5024 2.8 nM 12% 21%
[0294] AL-DUP 5024 and AL-DUP 5048 were chosen for further
investigations.
Example 6
siRNA Duplexes were Modified and Exhibited Improved Resistance to
Nucleases
[0295] The siRNA duplexes AL-DUP 5024 and AL-DUP 5048 were altered
with various chemical modifications in an attempt to enhance the
resistance of the oligonucleotide strands against degradation by
nucleases present in biological fluids, such as, for example, serum
and the intracellular medium. Specifically, phosphorothioate
linkages were introduced between positions 21 and 22 and between
positions 22 and 23 of the antisense strands, and/or between
positions 20 and 21 of the sense strands (see Table 10), thereby
increasing the stability of the siRNAs against exonucleolytic
degradation.
TABLE-US-00012 TABLE 10 siRNAs for stability assays SEQ. SEQ Duplex
ID ID descriptor No. Sense strand sequence No. .Antisense strand
sequence SiRNA duplexes derived from AL-DUP 5024 AL-DUP 5163 241
gguguauggcuucaacccug(chol) 242 aggguugaagccauacaccumcmu AL-DUP 5164
243 ggumgumaumggcumucmaacccumg(chol) 244
magggumumgaagccmaumacmaccucu AL-DUP 5165 241
gguguauggcuucaacccug(chol) 244 magggumumgaagccmaumacmaccucu AL-DUP
5166 243 ggumgumaumggcumucmaacccumg(chol) 242
aggguugaagccauacaccumcmu AL-DUP 5180 249 ggumgumaumggcumucmaacccumg
242 aggguugaagccauacaccumcmu AL-DUP 5181 249
ggumgumaumggcumucmaacccumg 244 magggumumgaagccmaumacmaccucu SiRNA
duplexes derived from AL-DUP 5048 AL-DUP 5167 253
ucaucacacugaauaccaau(chol) 254 uugguauucagugugaugacmamc AL-DUP 5168
255 ucmaucmacmacumgaaumaccmaau(chol) 256
umumggumaumucmagumgumgaumgacmac AL-DUP 5169 253
ucaucacacugaauaccaau(chol) 256 umumggumaumucmagumgumgaumgacmac
AL-DUP 5170 255 ucmaucmacmacumgaaumaccmaau(chol) 254
uugguauucagugugaugacmamc AL-DUP 5182 261 ucmaucmacmacumgaaumaccmaau
254 uugguauucagugugaugacmamc AL-DUP 5183 261
ucmaucmacmacumgaaumaccmaau 256 umumggumaumucmagumgumgaumgacmac m =
2'O-methyl modification; "(chol)" indicates cholesterol conjugated
to the 3'-end via a pyrrolidine linker comprising a
phosphorothioate
[0296] Previously, this laboratory identified certain sequence
motifs in siRNA duplexes which are particularly prone to
degradative attack by endonucleases (see co-owned and co-pending
application U.S. 60/574,744). Specifically, these motifs are
5'-UA-3', 5'-UG-3', 5'-CA-3', 5'-UU-3', and 5'-CC-3'. SiRNAs
comprising these sequence motifs can be stabilized towards
degradative attack by endonucleases by replacing the 2'-OH of the
ribose subunit of the 5'-most nucleotide in these dinucleotide
motifs with 2'-O--CH.sub.3 (also referred to herein as 2'-O-Methyl
or 2'-O-Me). Hence, siRNAs were synthesized wherein the respective
nucleotides bear a 2'-O-Me group in all occurrences of these
dinucleotide motifs, except for occurrences of 5'-CC-3', on either
the sense strand, the antisense strand, or both.
[0297] A further modification tested was the conjugation of a
cholesterol moiety to the 3'-end of the sense strand of the siRNAs
(see FIG. 1). This modification is thought to facilitate the uptake
of RNA into cells (Manoharan, M. et al., Antisense and Nucleic Acid
Drug Development 2002, 12:103-128).
[0298] The siRNA duplexes listed in Table 10 were synthesized and
tested for their stability towards nucleolytic degradation in the
serum incubation assay, as well as their activity in reducing the
amount of ApoB protein secreted into supernatant by cultured NmuLi
cells.
[0299] The nucleotide sequences of siRNA AL-DUP 5024, AL-DUP 5163,
AL-DUP 5164, AL-DUP 5165, AL-DUP 5166, AL-DUP 5180, and AL-DUP 5181
are identical except for the following:
[0300] AL-DUP 5024 consists entirely of unmodified nucleotides;
[0301] AL-DUP 5163 bears 2'-O-Me groups in positions 21 and 22 and
phosphorothioate linkages between positions 21 and 22, and 22 and
23, of the antisense strand, and a cholesterol moiety conjugated to
the 3'-end of the sense strand;
[0302] AL-DUP 5164 bears 2'-O-Me groups in positions 4, 6, 8, 12,
14, and 20 of its sense strand and in positions 1, 6, 7, 13, 15,
and 17 of its antisense strand, phosphorothioate linkages between
positions 21 and 22, and 22 and 23, of the antisense strand, and a
cholesterol moiety conjugated to the 3'-end of the sense
strand;
[0303] AL-DUP 5165 bears 2'-O-Me groups in positions 1, 6, 7, 13,
15, and 17 of its antisense strand, phosphorothioate linkages
between positions 21 and 22, and 22 and 23, of the antisense
strand, and a cholesterol moiety conjugated to the 3'-end of the
sense strand;
[0304] AL-DUP 5166 bears 2'-O-Me modifications in positions 4, 6,
8, 12, 14, and 20 of its sense strand and in positions 21 and 22 of
its antisense strand, phosphorothioate linkages between positions
21 and 22, and 22 and 23, of the antisense strand, and a
cholesterol moiety conjugated to the 3'-end of the sense
strand;
[0305] AL-DUP 5180 bears 2'-O-Me modifications in positions 4, 6,
8, 12, 14, and 20 of its sense strand and in positions 21 and 22 of
its antisense strand, and phosphorothioate linkages between
positions 21 and 22, and 22 and 23, of the antisense strand and
between position 20 and 21 of the sense strand; and
[0306] AL-DUP 5181 bears 2'-O-Me modifications in positions 4, 6,
8, 12, 14, and 20 of its sense strand and in positions 1, 6, 7, 13,
15, and 17 of its antisense strand, and phosphorothioate linkages
between positions 21 and 22, and 22 and 23, of the antisense strand
and between position 20 and 21 of the sense strand.
[0307] The nucleotide sequences of siRNA duplexes AL-DUP 5048,
AL-DUP 5167, AL-DUP 5168, AL-DUP 5169, AL-DUP 5170, AL-DUP 5182,
and AL-DUP 5183 are identical except that:
[0308] AL-DUP 5048 consists entirely of unmodified nucleotides;
[0309] AL-DUP 5167 bears 2'-O-Me groups in positions 21 and 22 and
phosphorothioate linkages between positions 21 and 22, and 22 and
23, of the antisense strand, and a cholesterol moiety conjugated to
the 3'-end of the sense strand;
[0310] AL-DUP 5168 bears 2'-O-Me groups in positions 3, 6, 8, 11,
15, and 18 of its sense strand and positions 2, 3, 6, 8, 10, 13,
15, 18, and 21 of its antisense strand, phosphorothioate linkages
between positions 21 and 22, and 22 and 23, of the antisense
strand, and a cholesterol moiety conjugated to the 3'-end of the
sense strand;
[0311] AL-DUP 5169 bears 2'-O-Me groups in positions 2, 3, 6, 8,
10, 13, 15, 18, and 21 of its antisense strand, phosphorothioate
linkages between positions 21 and 22, and 22 and 23, of the
antisense strand, and a cholesterol moiety conjugated to the 3'-end
of the sense strand;
[0312] AL-DUP 5170 bears 2'-O-Me modifications in positions 3, 6,
8, 11, 15, and 18 of its sense strand and in positions 21 and 22 of
its antisense strand, phosphorothioate linkages between positions
21 and 22, and 22 and 23, of the antisense strand, and a
cholesterol moiety conjugated to the 3'-end of the sense
strand;
[0313] AL-DUP 5182 bears 2'-O-Me modifications in positions 3, 6,
8, 11, 15, and 18 of its sense strand and in positions 21 and 22 of
its antisense strand, and phosphorothioate linkages between
positions 21 and 22, and 22 and 23, of the antisense strand and
between position 20 and 21 of the sense strand; and
[0314] AL-DUP 5183 bears 2'-O-Me modifications in positions 3, 6,
8, 11, 15, and 18 of its sense strand and in positions 2, 3, 6, 8,
10, 13, 15, 18, and 21 of its antisense strand, and
phosphorothioate linkages between positions 21 and 22, and 22 and
23, of the antisense strand and between position 20 and 21 of the
sense strand.
[0315] Stability of the siRNAs listed in Table 10 was tested in
mouse and 95% human serum. Mouse serum was obtained from Sigma
(Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany, cat. No. M5905)
or Charles River (Charles River Laboratories, Sulzfeld, Germany,
cat. No. MASER). Assay results reported herein were consistent
among the different serum sources tested. To test the stability of
the modified siRNA in human serum, blood from eight human
volunteers (270 mL) was collected and kept at room temperature for
3 hours. The blood pool was then centrifuged at 20.degree. C. and
3000 rcf using Megafuge 1.0 (Heraeus Instruments, Kendro Laboratory
Products GmbH, Langenselbold) to separate serum from the cellular
fraction. The supernatant was stored in aliquots at -20.degree. C.
and used as needed. Human serum obtained from Sigma (Sigma-Aldrich
Chemie GmbH, Taufkirchen, Germany, cat. No. H1513) was used in
control assays.
[0316] Double stranded RNAs (300 pmol, ca. 4.2 .mu.g) dissolved in
6 .mu.l PBS were added to 60 .mu.l human serum, and the mixture was
incubated at 37.degree. C. for varying extents of time, e.g. 0, 15,
or 30 minutes, or 1, 2, 4, 8, 16, or 24 hours. Subsequently, the
whole tube containing the RNA/serum solution was frozen in liquid
nitrogen and stored at -80.degree. C.
[0317] For analysis of non-cholesterol conjugated siRNAs, the
frozen samples were placed on ice and 450 .mu.l of 0.5 M NaCl was
added. After complete thawing, the solution was transferred to
Phase-Lock Gel tubes (Eppendorf, Hamburg, Germany; cat. No. 0032
005.152), mixed with 500 .mu.l 50% phenol, 48% chloroform, 2%
isoamylacohol (Carl Roth GmbH & Co KG, Karlsruhe, Germany, cat.
No. A156.2), and an additional 300 .mu.l Chloroform were added. The
tubes were vortexed vigorously for 30 seconds and subsequently
centrifuged for 15 min at 16,200 rcf at 4.degree. C. The aqueous
supernatant was transferred to a fresh tube and mixed with 40 .mu.l
3M Na-acetate pH 5.2, 1 .mu.l GlycoBlue (Ambion, Tex., USA; cat.
No. 9516) and 1 ml Ethanol 95%. RNA was precipitated overnight at
-20.degree. C.
[0318] Cholesterol-conjugated siRNAs were isolated by hot
phenol-extraction in presence of SDS (Sodium Dodecylsulfate). The
serum sample (66 .mu.l) was mixed with 200 .mu.l RNA buffer (0.5%
SDS, 10 mM EDTA, 10 mM Tris pH7.5) and 200 .mu.l water-saturated
phenol (Carl Roth GmbH & Co KG Karlsruhe, Germany; cat. No.
A980.1). The reaction tube was incubated for 20 min at 65.degree.
C. In order to achieve phase separation, the tubes were placed on
ice for 5 min and subsequently centrifuged for 10 min at 16,200 rcf
at 4.degree. C. The aqueous phase was transferred to a fresh tube.
The remaining phenol phase was extracted a second time with 150
.mu.l RNA portion and vigorous vortexing for 10 sec. The tubes were
placed on ice for 2 min and then centrifuged for 10 min at 16,200
rcf at 4.degree. C. The aqueous phase of the second extraction was
transferred and combined with the supernatant of the first
extraction. The RNA was precipitated by adding 2 .mu.l GlycoBlue
(Ambion, Austin, Tex., USA; Cat. No. 9516) and 1 ml Ethanol 95%.
Precipitation of RNA was brought to completion overnight at
-20.degree. C.
[0319] Isolated RNA was analyzed by denaturing gel electrophoresis.
Tubes containing the precipitated RNA were centrifuged for 10 min
at 16,200 rcf at 4.degree. C. The supernatant was removed and
discarded. The RNA pellet was washed with 400 .mu.l 70% Ethanol,
and re-pelleted by centrifugation for 5 min at 16,200 rcf at
4.degree. C. All liquid was removed and the pellet was dissolved in
20 .mu.l STOP buffer (95% formamide, 5% EDTA 0.5M, 0.02% xylene
cyanol). The samples were boiled for 3 min at 92.degree. C. and
chilled quickly on ice. 10 .mu.l were loaded on a denaturing 14%
polyacrylamide gel (6M Urea, 20% formamide, Carl Roth GmbH & Co
KG Karlsruhe, Germany). The RNA was separated for about 2 h at 45
mA. RNA bands were visualized by staining with the "stains-all"
reagent (Sigma-Aldrich Chemie GmbH, Steinheim, Germany, cat. no.
E9379) according to manufacturer's instructions.
[0320] While the unmodified AL-DUP 5024 was almost completely
degraded after 1 h of incubation with mouse and human serum, the
modified siRNAs were more resistant to degradation (see FIG. 3).
Following electrophoretic separation, full length RNA was stained
with stains-all reagent for up to 3 hours for AL-DUP 5163, and up
to 6 hours of incubation for AL-DUP 5164, AL-DUP 5165, AL-DUP 5166,
AL-DUP 5180, and AL-DUP 5181. The greatest stabilizing effect was
seen in AL-DUP 5164, AL-DUP 5166, and AL-DUP 5181, indicating that
the modification of sites prone to degradation in the sense strand
was most effective. Additional modification of the antisense strand
imparted only a small additional stabilizing effect. (See FIG.
3)
[0321] Similarly, the unmodified AL-DUP 5048 was almost completely
degraded after 1 h of incubation with mouse serum, while the
modified dsRNAs were less sensitive to degradation. Following
electrophoretic separation, full length RNA was stained with the
stains-all reagent after up to 3 hours for AL-DUP 5167, AL-DUP
5170, and AL-DUP 5182, and up to 6 hours for AL-DUP 5169, and up to
24 hours for AL-DUP 5168 and AL-DUP 5183. (See FIG. 3)
[0322] The siRNA duplexes listed in Table 10 were tested for their
efficacy in reducing ApoB protein secretion into supernatant by
cultured HepG2 cells in order to select the most active duplexes
for further examination in vivo.
[0323] The silencing activity of cholesterol modified siRNAs
specific for ApoB in in vitro assays in HepG2 cells was comparable
to that of unmodified ApoB-specific siRNAs. At 200 nM
concentrations the two unconjugated siRNAs AL-DUP 5024 and AL-DUP
5048 reduced murine ApoB mRNA levels by 84.+-.9% and 72.+-.9%,
respectively, whereas the corresponding conjugated and modified
siRNAs AL-DUP 5167 and AL-DUP 5163 had an inhibitory activity of
61.+-.8% % and 68.+-.9%, respectively.
[0324] FIGS. 5A through 5L show dose-response curves of ApoB
protein secretion into supernatant of cultured human HepG2 cells
incubated with media containing 100, 33, 11, 3.7, 1.2, 0.4, 0.14,
or 0.05 nM of the ApoB-specific siRNA duplexes. The response is
expressed as the ratio of ApoB protein concentrations in the
supernatant of cells treated with the ApoB-specific siRNA duplex to
the ApoB concentration in the supernatant of cells treated with an
unspecific control siRNA duplex. On the basis of these results,
AL-DUP 5163, AL-DUP 5165, AL-DUP 5166 and AL-DUP 5167 were chosen
for testing in mice (see results below).
Example 7
Modified siRNA Duplexes Reduced ApoB mRNA Amounts in Tissue
Sections from Liver and Jejunum, and ApoB Protein's Cholesterol
Levels in Serum of Male C57Bl/6 Mice
[0325] Bolus dosing of siRNAs in mice was performed by tail vein
injection using a 27 G needle. SiRNAs were dissolved in PBS at a
concentration allowing the delivery of the intended dose in 8
.mu.l/g body weight. Mice were kept under an infrared lamp for
approximately 3 min prior to dosing to ease injection.
[0326] Pre-treatment blood samples were collected several days
before dosing by collecting 4-7 drops from the tail vein. Upon
sacrifice by CO.sub.2-asphyxiation, ca. 0.7 ml blood was collected
by heart puncture, the liver and jejunum were collected, and tissue
aliquots of 20-40 mg were frozen in liquid nitrogen and stored at
-80.degree. C. until analysis.
[0327] ApoB100 mRNA levels were measured by branched-DNA-assay as
described above. Triplicate samples of frozen tissue sections
(liver or jejunum) of about 10-30 mg each were homogenized by
sonication (Bandelin Sonopuls HD 2070, BANDELIN electronic GmbH
& Co. KG, Berlin, Germany) in 1 ml of Tissue and Cell Lysis
solution (Epicentre, Madison, Wis., USA, cat. No. MTC096H)
containing 84 .mu.g/ml Proteinase K (Epicentre, Madison, Wis., USA,
cat. No. MPRK092) using 3-9 pulses of 0.9 sec each at an amplitude
of ca. 150 .mu.m. Lysates were kept at -80.degree. C. for at least
12 h (overnight) before analysis.
[0328] Frozen lysates were thawed at room temperature, and ApoB and
GAPDH mRNA quantified using the Quantigene Explore Kit according to
manufacturer's instructions. Nucleic acid sequences for Capture
Extender (CE), Label Extender (LE) and blocking (BL) probes were
selected from the nucleic acid sequences of ApoB and GAPDH with the
help of the QuantiGene ProbeDesigner Software 2.0 (Genospectra,
Fremont, Calif., USA, cat. No. QG-002-02). Probe nucleotide
sequences used in ApoB quantization are shown in Table 4. Probe
nucleotide sequences used in GAPDH quantization are shown in Table
6.
[0329] The ratio of ApoB mRNA to GAPDH mRNA in tissue samples was
averaged over each treatment group and compared to an untreated
control group or a control group treated with an unrelated siRNA
duplex.
[0330] ELISA assays were performed to quantitate the amount of
ApoB100 protein in mouse serum. To perform the assay, a 96 well
plate was coated with 100 .mu.l of the mouse ApoB-100-specific
monoclonal antibody LF3 (25 .mu.g/ml; Zlot, C. H. et al., J. Lipid
Res. 1999, 40:76-84) and the plate was incubated for 2 hours at
37.degree. C. The plate was washed three times with phosphate
buffered saline (PBS) (PS Dulbecco without Ca.sup.2+, Mg.sup.2+,
Biochrom AG, Berlin, Germany, cat. No. L182-05), and then the
remaining binding sites were blocked by adding 300 .mu.l PBS
containing 3% bovine serum albumin (BSA) (Carl Roth GmbH & Co
KG, Karlsruhe, Germany, cat. no. 8076.2) to each well. Plates were
incubated for 1 hour at room temperature. The plate was then washed
5 times with PBS. 0.2 .mu.l mouse serum diluted in 100 .mu.l PBS
containing 0.1% Tween (Carl Roth GmbH & Co KG, Karlsruhe,
Germany, cat. No. 9127.1) and 3% BSA was added to each well. After
an incubation of 2 hours at 37.degree. C. the plate was washed 5
times with PBS. 100 .mu.l of a 1:500 dilution of the polyclonal
rabbit anti-mouse apolipoprotein B48/100 antibody (Acris Antibodies
GmbH, Hiddenheim, Germany, cat. no. BP2050) was added to the wells
and incubated for 2 hours at 37.degree. C. After washing the plate
5 times with PBS, 100 .mu.l of a donkey anti-rabbit IgG conjugated
to horse radish peroxidase (Santa Cruz Biotechnology, Santa Cruz,
Calif., USA, cat. no. sc2004) was added and incubated for 1 hour at
37.degree. C. The plate was washed 5 times with PBS and wells were
incubated with 0.9 mg/ml OPD (o-phenylendiamine dihydrochloride,
Merck Biosciences GmbH, Bad Soden, Germany cat. No. 523121) in 24
mmol/L citric acid buffer (Sigma-Aldrich, Taufkirchen, Germany,
cat. no. C1909-1KG), pH 5.0 containing 0.03% hydrogen peroxide
(Merck Biosciences GmbH, Bad Soden, Germany, cat. No. 386790). The
enzyme reaction was stopped by adding 0.5 mol/L H.sub.2SO.sub.4
(Merck KgaA, Darmstadt, Germany, cat. No. 100731) and absorbance at
490 nm was measured on a spectrophotometer (Perkin Elmer Wallac
Victor3 1420 multilabel reader, PerkinElmer LAS GmbH, Rodgau,
Germany).
[0331] Total serum cholesterol in mouse serum was measured using
the Cholesterol FS reagent kit (DiaSys Diagnostic Systems GmbH,
Holzheim, Germany) according to manufacturer's instructions.
Measurements were taken on a spectral photometer (DU 640B, Beckman
Coulter GmbH, Unterschlei.beta.heim, Germany).
[0332] S1-nuclease protection assay were used to detect siRNAs in
liver and jejunum tissue and in serum following injections. Small
pieces (10-30 mg) of animal tissue were homogenized as described
above for the branched-DNA assay. These lysates were either
processed immediately, or stored at -80.degree. C. and thawed at
room temperature prior to assay performance. 100 .mu.l lysate was
transferred to a fresh reaction tube and mixed with 200 .mu.l STE
(Sodium chloride-TRIS-EDTA buffer; 500 mM NaCl, 9 mM Tris pH 7.5,
0.9 mM EDTA) and 200 .mu.l phenol (TRIS-EDTA saturated phenol,
Roti-phenol, Carl Roth GmbH & Co KG, Karlsruhe, Germany, cat.
no. 0038.1). The tubes were vigorously mixed on a Vortex Genie 2
(Scientific Industries, Inc., Bohemia, N.Y., USA, cat. no. SI-0256)
at maximum speed for 30 seconds, and subsequently centrifuged for
10 min at 16,200 rcf and 4.degree. C. About 310 .mu.l aqueous
supernatant was carefully aspired and transferred to a new reaction
tube, mixed with 50 .mu.g E. coli tRNA (Roche Diagnostics,
Penzberg, Germany; cat. No. 109 541) and 900 .mu.l Ethanol 95%.
Precipitation of RNA was continued over night at -20.degree. C.
[0333] DNA probes for use in the S1-nuclease protection assays were
radioactively labelled. Probes of 25 to 27 nucleotides length
corresponded to the 21 nucleotide sense-strand sequence of the
siRNA molecules, but contained an additional 4 to 6 nucleotides at
their 3'-end serving as non-complementary extension. The DNA
oligonucleotides probes were phosphorylated with .gamma.-.sup.32P
ATP to introduce a radioactive phosphate group at their 5'-end.
Fifteen picomoles of the respective probe were mixed with 50 .mu.Ci
of .gamma.-.sup.32P ATP (Amersham GE-Healthcare, Freiburg, Germany,
cat. no. AA0018) and 10 U Polynucleotide kinase (New England
Biolabs, Frankfurt, Germany, MO201 S) were mixed in a total volume
of 50 .mu.l Polynucleotide kinase buffer (New England Biolabs,
Frankfurt, Germany, cat. no. MO201S). This solution was incubated
at 37.degree. C. for 1 hour. The labelling reaction was terminated
by passing the reaction mixture through a Microspin G-25 desalting
column following instructions by the manufacturer (Amersham
GE-Healthcare, Freiburg, Germany, cat. no. 27-5325-01). The
resulting probe solutions were used within 1-3 days.
[0334] To detect siRNAs from mouse tissue lysates, precipitated
total RNA from the lysates was centrifuged for 10 min at 16,200 rcf
and 4.degree. C. The supernatant was carefully removed and
discarded while keeping the nucleic acid pellet. This pellet was
first resuspended in 50 .mu.l S1-hybridization buffer (300 mM NaCl,
1 mM EDTA, 38 mM HEPES pH 7.0, 0.1% Triton X-100) and then 1 .mu.l
of radioactive DNA probe solution was added. The hybridization
reaction mixture was heated to 92.degree. C. for 2 min. The
reaction tubes were immediately transferred to a heating block kept
at 37.degree. C. and further incubated for 30 min. The
hybridization was continued at room temperature for an additional 2
hours.
[0335] For the determination of siRNA concentrations in serum, 1
.mu.l of serum was mixed with 50 .mu.l S1-hybridization buffer and
1 .mu.l of radioactive DNA probe, and the hybridization continued
as above.
[0336] The following probes were used:
[0337] For AL-DUP 3001 and AL-DUP 5386:
TABLE-US-00013 SEQ. ID NO. 265 5'- AACTGTGTGTGAGAGGTCCTTCTT-3'
[0338] For AL-DUP 5311
TABLE-US-00014 SEQ. ID NO. 266 5'-
TGATCAGACTCAATACGAATTCTTCTT-3'
[0339] For siRNAs derived from AL-DUP 5048 (AL-DUP 5048, AL-DUP
5167, AL-DUP 5168, AL-DUP 5169, AL-DUP 5170, AL-DUP 5182, AL-DUP
5183, AL-DUP 5385, AL-DUP 5546)
TABLE-US-00015 SEQ. ID NO. 267 5'-
TCATCACACTGAATACCAATTCTTCT-3'
[0340] For siRNAs derived from AL-DUP 5024 (AL-DUP 5024, AL-DUP
5163, AL-DUP 5164, AL-DUP 5165, AL-DUP 5166, AL-DUP 5180, AL-DUP
5181)
TABLE-US-00016 SEQ. ID NO. 268 5'-
GGTGTATGGCTTCAACCCTGTCTTCT-3'
[0341] For siRNAs derived from AL-DUP 5002 (AL-DUP 5536, AL-DUP
5537)
TABLE-US-00017 SEQ. ID NO. 245 5'-
ATTGATTGACCTGTCCATTCTCTTCTT-3'
[0342] For siRNAs derived from AL-DUP 5035 (AL-DUP 5538, AL-DUP
5539)
TABLE-US-00018 SEQ. ID NO. 246 5'-
ACCAACTTCTTCCACGAGTCTCTTCTT-3'
[0343] For siRNAs derived from AL-DUP 5089 (AL-DUP 5540, AL-DUP
5541)
TABLE-US-00019 SEQ. ID NO. 247 5'-
AGTTTGTGACAAATATGGGCTCTTCTT-3'
[0344] For siRNAs derived from AL-DUP 5097 (AL-DUP 5542, AL-DUP
5543)
TABLE-US-00020 SEQ. ID NO. 248 5'-
TTTACAAGCCTTGGTTCAGTTCTTCTT-3'
[0345] For siRNAs derived from AL-DUP 5098 (AL-DUP 5544, AL-DUP
5545)
TABLE-US-00021 SEQ. ID NO. 250 5'-
GAATCTTATATTTGATCCAATCTTCTT-3'
[0346] In addition, two probes hybridizing with micro-RNAs
endogenously expressed in liver (miRNA122) and jejunum (miRNA143)
were used as a loading control.
[0347] For miRNA 122:
TABLE-US-00022 SEQ. ID NO. 269 5'-
AACACCATTGTCACACTCCATCTTCTT-3'
[0348] For miRNA 143:
TABLE-US-00023 SEQ. ID NO. 270 5'-
AGCTACAGTGCTTCATCTCATCTTCTT-3'
[0349] After hybridization, 450 .mu.l of S1-nuclease digestion mix
was added to each tube (450 .mu.l S1-reaction mix: 333 mM NaCl, 2.2
mM Zn-acetate, 66.7 mM Na-acetate pH 4.5, 0.02% Triton X-100 and
100 U S1-Nuclease; Amersham GE-Healthcare, Freiburg, Germany; cat.
no. E2410Y) to degrade any unhybridized probe. The digestion
reaction mixture was incubated at 37.degree. C. for 30 min. The
reaction digestion was terminated by the addition of 30 .mu.g tRNA
(Roche Diagnostics, Penzberg, Germany; 109 541) in 7 .mu.l of 500
mM EDTA, pH 8.0, and 900 .mu.l Ethanol 95%. The protected probes
were precipitated at -20.degree. C. over night or at -80.degree. C.
for 90 min.
[0350] Following precipitation, the protected probes were analyzed
by denaturing gel electrophoresis. The precipitated duplexed RNA
was centrifuged for 10 min at 16,200 rcf and 4.degree. C. The
supernatant was carefully removed and discarded. The pellet was
dissolved in 12 .mu.l STOP buffer (95% formamide, 5% EDTA 0.5M,
0.02% xylene cyanol). The tubes were heated to 92.degree. C. for 2
min and then immediately chilled on ice. 4 .mu.l of the solution
were loaded per lane of a denaturing sequencing gel (12.5%
acrylamide, 1.times. standard TBE buffer, 19 cm.times.20
cm.times.0.4 mm Length.times.Width.times.Depth; Rotiphorese DNA
sequencing system, Carl Roth GmbH & Co KG, Karlsruhe, Germany,
cat. no. A431.1). The gel was run for 45 min at 600 V corresponding
to a voltage gradient of approximately 30 V/cm (EPS 3501XL,
Amersham Biosciences, Uppsala, Sweden; cat. no. 18-1130-05). The
gel was dried on paper and exposed overnight to a general purpose
phosphor screen imager (Amersham GE-Healthcare, Freiburg, Germany;
cat. no. 63-0034-88). On the following day, radioactive bands were
visualized on a Typhoon 9200 high performance imager (Amersham
GE-Healthcare, Freiburg, Germany; cat. no. 63-0038-49).
Quantitation of radioactive band intensity was performed using the
ImageQuant TL software version 2003.01 supplied with Typhoon 9200
imager by comparison to a dilution series of 60, 20, 6.6, and 2.2
fmol of the respective radioactive probe loaded onto the gel.
[0351] All animal experiments, except those involving animals
transgenic for the expression of human ApoB described below, were
carried out in compliance with the regulations of the European
Convention for the Protection of Vertebrate Animals used for
Experimental and other Scientific Purposes. Male C57Bl/6 mice were
obtained from Charles River Laboratories, Sulzfeld, Germany, and
acclimatized for at least 5 days before use. Animals were housed at
22.+-.2.degree. C. and 55.+-.10% rel. humidity. Day/night rhythm
was 12 hours, changing at 6:00 am (light) and 6:00 pm (dark).
Animals were fed Ssniff R/M-H chow (Ssniff Spezialdiaten GmbH,
Soest, Germany, cat. No. V1531) ad libitum, unless specifically
specified otherwise below.
[0352] The following experimental protocols were performed.
[0353] A.) Three groups of 7 animals, age 3.5 months, received
daily doses of 50 mg/kg on three consecutive days of either AL-DUP
5163, AL-DUP 5166 (sequences see Table 10), or an equivalent amount
of carrier, and were sacrificed on the fourth day. Total serum
cholesterol, serum ApoB100 concentration, and liver and jejunum
ApoB mRNA levels were determined.
[0354] The 2'-O-methyl modification of the nucleotides in positions
4, 6, 8, 12, 14, and 20 in the sense strand of AL-DUP 5166 as
compared to the otherwise identical AL-DUP 5163 afforded greater
stability to AL-DUP 5166 with respect to its degradation in serum
(see FIG. 3). This experiment was designed to test the ability of
siRNA specific for mouse ApoB to down-regulate the expression of
the ApoB gene in the liver and jejunum of mice, and to lower ApoB
protein levels and cholesterol levels in serum. This experiment
also tested whether an siRNA bearing 2'-O-Me modifications on its
sense strand, which increases its stability in biological serum was
more potent in down-regulating the expression of ApoB, than an
siRNA lacking the 2'OMe sense strand modification.
[0355] ApoB mRNA levels in liver and jejunum tissue were assayed by
the branched DNA assay. AL-DUP 5163 was found to lower the levels
of ApoB mRNA in samples of liver tissue to 50.+-.13% of the levels
present in liver tissue of control animals. Levels of ApoB mRNA in
jejunum were lowered to 40.+-.6% of the levels in control
animals.
[0356] AL-DUP 5166 was found to lower the levels of ApoB mRNA in
liver tissue to 59.+-.9% of the mRNA levels in tissue of control
animals. Levels of ApoB mRNA in jejunum were lowered to 14.+-.3% of
the levels in control animals.
[0357] B.) Two groups of 7 animals, age 3.5 months were treated for
three consecutive days with daily doses of 50 mg/kg of either
AL-DUP 5167 (sequences see Table 10) or an equivalent amount of
carrier. The mice were sacrificed on the fourth day. Total serum
cholesterol, serum ApoB 100 concentration, and liver and jejunum
ApoB mRNA levels were determined.
[0358] ApoB mRNA levels were determined by branched DNA assay.
AL-DUP 5167 was found to lower the levels of ApoB mRNA present in
samples of liver tissue from treated mice to 41.+-.6% of the mRNA
levels present in liver tissue of control animals. Levels of ApoB
mRNA in jejunum were lowered to 29.+-.9% of the levels in control
animals. Serum ApoB protein concentration in mouse sera was
essentially unchanged at 101.+-.9% of control levels. Serum
cholesterol was lowered to 60.+-.22% of carrier controls.
[0359] C.) Three groups of 7 animals, age 2.5 months, received
daily doses of 50 mg/kg, on three consecutive days, of AL-DUP 5165
or an equivalent amount of carrier, and were sacrificed on the
fourth day. Total serum cholesterol, serum ApoB 100 concentration,
and liver ApoB mRNA levels were determined.
[0360] The 2'-O-Me modification of the nucleotides in positions 1,
6, 7, 13, 15, and 17 of its antisense strand of AL-DUP 5165 as
compared to the otherwise identical AL-DUP 5163 (sequences see
Table 10) afforded greater stability to AL-DUP 5165 with respect to
its degradation in serum (see FIG. 3), but the stabilizing effect
was not quite as strong as seen in AL-DUP 5166. This experiment
compared the ability of siRNA specific for mouse ApoB, and bearing
stabilizing modifications on the antisense strand, to down-regulate
the expression of the ApoB gene in the liver and jejunum of mice,
and lower serum ApoB and cholesterol levels. The experiment also
tested whether an siRNA modified to possess increased stability in
serum was more potent in down-regulating the expression of
ApoB.
[0361] The branched DNA assay was used to measure ApoB mRNA levels.
AL-DUP 5165 was found to lower the levels of ApoB mRNA in liver
tissue from treated mice to 68.+-.12% of the mRNA levels present in
liver tissue of control animals receiving carrier only. Serum ApoB
protein concentration in mouse sera was lowered to 63.+-.6% of
control levels. Serum cholesterol was found unchanged at 99.+-.26%
of carrier control levels.
[0362] D.) Four groups of 6 animals, age 2.5 months, received daily
doses of 50 mg/kg, on three consecutive days, of either AL-DUP
5167, AL-DUP 3001, AL-DUP 5311, or an equivalent amount of carrier,
and were sacrificed on the fourth day. Total serum cholesterol,
serum ApoB 100 concentration, and liver and jejunum ApoB mRNA
levels were determined.
[0363] The nucleotide sequences of AL-DUP 5167 is shown in Table
10. The sequences of AL-DUP 5311 and AL-DUP 3001 are as follows
TABLE-US-00024 AL-DUP 5311 SEQ. ID No. 271 Sense: 5'-
ugaucagacugaauacgaau(Chol)-3' SEQ. ID No. 272 Antisense: 5'-
uucguauugagucugaucacmamc-3' AL-DUP 3001 (SEQ. ID No. 273) Sense:
5'- aacugugugugagagguccu(Chol)-3' (SEQ. ID No. 274) Antisense: 5'-
ggaccucucacacacaguucgmcm-3'
[0364] AL-DUP 5311 represents a mouse ApoB mRNA mismatch siRNA to
AL-DUP 5167 where four G/C switches in positions 4, 10, 14, and 19
were made. This siRNA was a negative control for comparison with
AL-DUP 5167.
[0365] AL-DUP 3001 represents an unrelated control siRNA. The
sequence of positions 1 to 21 of the sense strand of AL-DUP 3001
corresponds to nucleotides 1252 to 1272 of cloning vector
pGL3-Basic (Promega GmbH, Mannheim, Germany, cat. no. E1751),
accession number U47295, and is part of a sequence encoding firefly
(Photinus pyralis) luciferase. AL-DUP 3001 was meant to serve as an
additional negative control to AL-DUP 5167.
[0366] This experiment was meant to confirm the earlier findings
obtained with AL-DUP 5167, and to further show that the effects
seen with AL-DUP 5167 are sequence-specific.
[0367] ApoB mRNA levels were determined by branched-DNA assay.
AL-DUP 5167 was found to lower the levels of ApoB mRNA in liver
tissue from treated mice to 36.+-.11% of the mRNA levels present in
liver tissue of control animals. Levels of ApoB mRNA in jejunum
were lowered to 27.+-.8% of the levels in control animals. Serum
ApoB protein concentration in mouse sera was lowered to
approximately 29.+-.16% of carrier control levels. Serum
cholesterol levels were essentially unchanged at 73.+-.35%.
[0368] AL-DUP 5311 was found to leave the levels of ApoB mRNA in
liver tissue from treated mice essentially unchanged at 95.+-.16%
of the mRNA levels present in liver tissue of control animals
injected with carrier. Levels of ApoB mRNA in jejunum were found
essentially unchanged at 120.+-.19% of the levels in control
animals. Serum ApoB protein concentration in mouse sera was
essentially unchanged at 109.+-.76% of carrier control levels.
Serum cholesterol levels were found essentially unchanged at
77.+-.43% of carrier controls.
[0369] AL-DUP 3001 was found to leave the levels of ApoB mRNA in
liver tissue from treated mice essentially unchanged at 79.+-.22%
of the mRNA levels in liver tissue of control animals receiving
carrier only. Levels of ApoB mRNA in jejunum were found essentially
unchanged at 130.+-.33% of the levels in control animals. Serum
ApoB protein concentration in mouse sera was found essentially
unchanged at 104.+-.55% of carrier control levels. Serum
cholesterol levels were found essentially unchanged at 108.+-.46%
of carrier control levels.
[0370] E.) Seven groups of six animals, age 2.5 months, received
daily doses of 50 mg/kg, on three consecutive days, of either
AL-DUP 5167, AL-DUP 3001, AL-DUP 5311, or an equivalent amount of
carrier, or daily doses of 10 mg/kg of AL-DUP 5167 on three
consecutive days, or daily doses of 2 mg/kg of AL-DUP 5167 on three
consecutive days, or a single dose of 50 mg/kg on day 1. The mice
were sacrificed on the fourth day. Another group of 6 animals
received an osmotic pump implant (Alzet 1007D, ALZET Osmotic Pumps
DURECT Corporation, Cupertino, Calif., USA) subcutaneously on their
back slightly posterior to the scapulae on day 1. The pump was set
to deliver 0.5 .mu.l/hr of a solution of 0.33 mg/.mu.l AL-DUP 5167
for 7 days, amounting to a daily dose of approximately 4 mg/kg body
weight per day per animal. This group of animals was sacrificed on
day 8. Total serum cholesterol, serum ApoB 100 concentration, and
liver and jejunum ApoB mRNA levels were determined.
[0371] The nucleotide sequence of AL-DUP 5167, AL-DUP 5311 and
AL-DUP 3001 are given above.
[0372] This experiment was meant to confirm the earlier findings
obtained with AL-DUP 5167, using carrier, a mismatched siRNA
(AL-DUP 5311), and an unrelated siRNA (AL-DUP 3001) as controls,
and to further determine whether bolus intravenous doses of 2 or 10
mg/kg body weight on three consecutive days, or a single dose of 50
mg/kg body weight on day 1, could suffice to elicit the effects
seen when dosing 50 mg/kg body weight intravenously on three
consecutive days in (C) and (D) above. Furthermore, this experiment
set out to compare these dosing regimens with continuous delivery
of a lower dose of 4 mg/kg body weight per day over 7 days from an
osmotic pump.
[0373] At a dose of 50 mg/kg body weight, administered
intravenously on three consecutive days followed by sacrifice on
day 4, AL-DUP 5167 was found to lower the levels of ApoB mRNA
present in samples of liver tissue from treated mice to 69.+-.17%
of the mRNA levels present in liver tissue of animals receiving
carrier only, and levels of ApoB mRNA in jejunum were lowered to
24.+-.8% of the levels in control animals, as determined by the
branched-DNA assay. Serum ApoB protein concentration in mouse sera
was lowered to 69.+-.9% of carrier control levels. Serum
cholesterol was found essentially unchanged at 95.+-.29% of carrier
control levels.
[0374] At a dose of 10 mg/kg body weight, administered
intravenously on three consecutive days followed by sacrifice on
day 4, AL-DUP 5167 was found to leave the levels of ApoB mRNA
present in samples of liver tissue from treated mice essentially
unchanged at 81.+-.32% of the mRNA levels present in liver tissue
of animals receiving carrier only, and levels of ApoB mRNA in
jejunum came to 62.+-.13% of the levels in control animals, as
determined by the branched-DNA assay. Serum ApoB protein
concentration in mouse sera was essentially unchanged at 101.+-.19%
of carrier control levels. Serum cholesterol was found essentially
unchanged at 101.+-.29% of carrier control levels.
[0375] At a dose of 2 mg/kg body weight, administered intravenously
on three consecutive days followed by sacrifice on day 4, AL-DUP
5167 was found to leave the levels of ApoB mRNA present in samples
of liver tissue from treated mice essentially unchanged at
109.+-.38% of the mRNA levels present in liver tissue of animals
receiving carrier only, and levels of ApoB mRNA in jejunum came to
97.+-.21% of the levels in control animals, as determined by the
branched-DNA assay. Serum ApoB protein concentration in mouse sera
was essentially unchanged at 115.+-.13% of carrier control levels.
Serum cholesterol was found essentially unchanged at 114.+-.26% of
carrier control levels.
[0376] At a dose of 50 mg/kg body weight, administered
intravenously once on day 1 followed by sacrifice on day 4, AL-DUP
5167 was found to lower the levels of ApoB mRNA present in samples
of liver tissue from treated mice to 41.+-.20% of the mRNA levels
present in liver tissue of animals receiving carrier only, and
levels of ApoB mRNA in jejunum were lowered to 62.+-.23% of the
levels in control animals, as determined by the branched-DNA assay.
Serum ApoB protein concentration in mouse sera was lowered to
52.+-.11% of carrier control levels. Serum cholesterol was found
essentially unchanged at 95.+-.25% of carrier control levels.
[0377] At a dose of 50 mg/kg body weight, administered
intravenously on three consecutive days followed by sacrifice on
day 4, AL-DUP 5311 was found to leave the levels of ApoB mRNA
present in samples of liver tissue from treated mice essentially
unchanged at 100.+-.16% of the mRNA levels present in liver tissue
of animals receiving carrier only, and levels of ApoB mRNA in
jejunum came to 100.+-.20% of the levels in control animals, as
determined by the branched-DNA assay. Serum ApoB protein
concentration in mouse sera was essentially unchanged at 97.+-.11%
of carrier control levels. Serum cholesterol was found essentially
unchanged at 129.+-.37% of carrier control levels.
[0378] At a dose of 50 mg/kg body weight, administered
intravenously on three consecutive days followed by sacrifice on
day 4, AL-DUP 3001 was found to leave the levels of ApoB mRNA
present in samples of liver tissue from treated mice essentially
unchanged at 97.+-.28% of the mRNA levels present in liver tissue
of animals receiving carrier only, and levels of ApoB mRNA in
jejunum came to 101.+-.16% of the levels in control animals, as
determined by the branched-DNA assay. Serum ApoB protein
concentration in mouse sera was lowered to 106.+-.6% of carrier
control levels. Serum cholesterol was found essentially unchanged
at 129.+-.43% of carrier control levels.
[0379] At a dose of 4 mg/kg body weight per day over 7 days
delivered from an osmotic pump, followed by sacrifice on day 8,
AL-DUP 5167 was found to leave the levels of ApoB mRNA present in
samples of liver tissue from treated mice essentially unchanged at
79.+-.24% of the mRNA levels present in liver tissue of animals
receiving carrier only, and levels of ApoB mRNA in jejunum came to
70.+-.19% of the levels in control animals, as determined by the
branched-DNA assay. Serum ApoB protein concentration in mouse sera
was lowered to 106.+-.6% of carrier control levels. Serum
cholesterol was found essentially unchanged at 129.+-.43% of
carrier control levels.
[0380] F.) Seven groups of six animals, age 2.5 months, received
one bolus dose of 50 mg/kg on day 1 of AL-DUP 5167. A control group
of six animals received an equivalent amount of carrier. Groups of
animals receiving siRNA were sacrificed 12, 24, 36, 60, 84 and 108
hours post-dosing. The control group receiving carrier was
sacrificed 84 hours post-dosing. Liver and jejunum ApoB mRNA levels
were determined.
[0381] The nucleotide sequence of AL-DUP 5167 is given above.
[0382] This experiment was designed to yield the time course of the
effects of AL-DUP 5167 on ApoB mRNA levels in liver and jejunum,
and on serum ApoB and cholesterol concentrations.
[0383] In animals sacrificed 12 hours post dosing of 50 mg/kg
AL-DUP 5167 intravenously, 100.+-.32% of the ApoB mRNA levels
present in liver tissue of animals receiving carrier only were
found in the liver, and 145.+-.78% of the ApoB mRNA levels present
in jejunum tissue of animals receiving carrier only were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
determined to 124.+-.14% of carrier control levels.
[0384] In animals sacrificed 24 hours post dosing of 50 mg/kg
AL-DUP 5167 intravenously, 85.+-.21% of the ApoB mRNA levels
present in liver tissue of animals receiving carrier only were
found in the liver, and 84.+-.32% of the ApoB mRNA levels present
in jejunum tissue of animals receiving carrier only were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
determined to 92.+-.52% of carrier control levels.
[0385] In animals sacrificed 36 hours post dosing of 50 mg/kg
AL-DUP 5167 intravenously, 64.+-.20% of the ApoB mRNA levels
present in liver tissue of animals receiving carrier only were
found in the liver, and 88.+-.19% of the ApoB mRNA levels present
in jejunum tissue of animals receiving carrier only were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to 55.+-.12% of carrier control levels.
[0386] In animals sacrificed 60 hours post dosing of 50 mg/kg
AL-DUP 5167 intravenously, 73.+-.10% of the ApoB mRNA levels
present in liver tissue of animals receiving carrier only were
found in the liver, and 41.+-.13% of the ApoB mRNA levels present
in jejunum tissue of animals receiving carrier only were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to 43.+-.16% of carrier control levels.
[0387] In animals sacrificed 84 hours post dosing of 50 mg/kg
AL-DUP 5167 intravenously, 72.+-.13% of the ApoB mRNA levels
present in liver tissue of animals receiving carrier only were
found in the liver, and 68.+-.22% of the ApoB mRNA levels present
in jejunum tissue of animals receiving carrier only were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to 54.+-.15% of carrier control levels.
[0388] In animals sacrificed 108 hours post dosing of 50 mg/kg
AL-DUP 5167 intravenously, 68.+-.15% of the ApoB mRNA levels
present in liver tissue of animals receiving carrier only were
found in the liver, and 85.+-.15% of the ApoB mRNA levels present
in jejunum tissue of animals receiving carrier only were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to 51.+-.8% of carrier control levels.
[0389] G.): Five groups of 10 animals, age 2.5 months, received
daily doses of 50 mg/kg body weight intravenously on three
consecutive days of either AL-DUP 5167, AL-DUP 5385, AL-DUP 5311,
AL-DUP 5386 or an equivalent amount of carrier, one group of 7
animals received AL-DUP 5163 by the same dosing regimen, and all
animals were sacrificed on the fourth day. Total serum cholesterol,
serum ApoB 100 concentration, and liver and jejunum ApoB mRNA
levels were determined. In addition, the amount of siRNA present in
samples of liver and jejunum was approximated by the 51-nuclease
protection assay (see FIG. 6).
[0390] The nucleotide sequences of AL-DUP 5167, AL-DUP 5163, and
AL-DUP 5311 are given above. The nucleotide sequences of AL-DUP
5385 and AL-DUP 5386 are:
TABLE-US-00025 AL-DUP 5385 SEQ. ID NO. 275 Sense: 5'-
ucaucacacugaauaccaau-3' SEQ. ID NO. 276 Antisense: 5'-
uugguauucagugugaugacmamc-3' AL-DUP 5386 SEQ. ID NO. 277 Sense: 5'-
aacugugugugagagguccu(Chol)-3' SEQ. ID NO. 278 Antisense: 5'-
ggaccucucacacacaguucmgmc-3'
[0391] AL-DUP 5385 is identical to AL-DUP 5167, except that it
bears no cholesterol moiety on the 3'-end of the sense strand, and
has a phosphorothioate linkage between positions 20 and 21 of the
sense strand. The latter phosphorothioate group was meant to confer
similar protection towards exonucleolytic degradation as the
phosphorothioate-bearing cholesterol modification (see FIG. 1).
[0392] AL-DUP 5386 is identical to AL-DUP 3001, except that the
2'-O-methyl-modification in position 23 of the antisense strand was
removed, and a 2'-O-methyl-modification was added in position 21.
This was believed to confer superior stabilization towards
degradation of AL-DUP 5386 over AL-DUP 3001.
[0393] This experiment was designed to confirm results obtained in
(E) above, to further compare the activity of the
cholesterol-conjugated AL-DUP 5167 to the activity of the otherwise
identical but cholesterol-lacking AL-DUP 5385, and to confirm that
the lack of ApoB mRNA expression inhibiting activity seen with
AL-DUP 3001 was not due to rapid degradation of AL-DUP 3001 in the
serum of treated mice.
[0394] AL-DUP 5167 was found to lower the levels of ApoB mRNA
present in samples of liver tissue from treated mice to 43.+-.6% of
the mRNA levels present in liver tissue of animals receiving
carrier only, and levels of ApoB mRNA in jejunum were lowered to
27.+-.10% of the levels in control animals, as determined by the
branched-DNA assay. Serum ApoB protein concentration in mouse sera
was lowered to 32.+-.14% of carrier control levels. Serum
cholesterol concentration in mouse sera was lowered to 63.+-.11% of
carrier control levels. Approx. 100-200 ng/of AL-DUP 5167 per g
tissue was detected in liver and jejunum tissue samples by the
S1-nuclease protection assay (FIG. 6A).
[0395] AL-DUP 5163 was found to lower the levels of ApoB mRNA
present in samples of liver tissue from treated mice to 64.+-.8% of
the mRNA levels present in liver tissue of animals receiving
carrier only, and levels of ApoB mRNA in jejunum were lowered to
49.+-.13% of the levels in control animals, as determined by the
branched-DNA assay. Serum ApoB protein concentration in mouse sera
was lowered to 66.+-.20% of carrier control levels. Serum
cholesterol concentration in mouse sera was essentially unchanged
at 94.+-.10% of carrier control levels. Approx. 50-150 ng/of AL-DUP
5163 per g tissue was detected in liver and jejunum tissue samples
by the 51-nuclease protection assay.
[0396] AL-DUP 5385 was found to leave the levels of ApoB mRNA
present in samples of liver tissue from treated mice essentially
unchanged at 84.+-.12% of the mRNA levels present in liver tissue
of animals receiving carrier only, and levels of ApoB mRNA in
jejunum came to 115.+-.25% of the levels in control animals, as
determined by the branched-DNA assay. Serum ApoB protein
concentration in mouse sera was found unchanged at 101.+-.24% of
carrier control levels. Serum cholesterol concentration in mouse
sera was essentially unchanged at 97.+-.10% of carrier control
levels. AL-DUP 5385 remained undetectable in liver and jejunum
tissue samples in the S1-nuclease protection assay (FIG. 6A).
[0397] AL-DUP 5311 was found to leave the levels of ApoB mRNA
present in samples of liver tissue from treated mice essentially
unchanged at 96.+-.16% of the mRNA levels present in liver tissue
of animals receiving carrier only, and levels of ApoB mRNA in
jejunum came to 96.+-.28% of the levels in control animals, as
determined by the branched-DNA assay. Serum ApoB protein
concentration in mouse sera was found unchanged at 102.+-.32% of
carrier control levels. Serum cholesterol concentration in mouse
sera was essentially unchanged at 104.+-.10% of carrier control
levels. Approx. 50-200 ng/of AL-DUP 5311 per g tissue was detected
in liver and jejunum tissue samples by the S1-nuclease protection
assay (FIG. 6A).
[0398] AL-DUP 5386 was found to leave the levels of ApoB mRNA
present in samples of liver tissue from treated mice essentially
unchanged at 89.+-.11% of the mRNA levels present in liver tissue
of animals receiving carrier only, and levels of ApoB mRNA in
jejunum came to 85.+-.14% of the levels in control animals, as
determined by the branched-DNA assay. Serum ApoB protein
concentration in mouse sera was found unchanged at 94.+-.31% of
carrier control levels. Serum cholesterol concentration in mouse
sera was essentially unchanged at 104.+-.10% of carrier control
levels. Approx. 50-200 ng/of AL-DUP 5386 per g tissue was detected
in liver and jejunum tissue samples by the S1-nuclease protection
assay (FIG. 6A).
[0399] H.): Six groups of 6 animals, age 2.5 months, received a
single intravenous bolus dose of 100, 50, 25 or 12.5 mg/kg body
weight of AL-DUP 5167, or an equivalent amount of carrier. Animals
were sacrificed 72 h post-dosing. Total serum cholesterol, serum
ApoB 100 concentration, and liver and jejunum ApoB mRNA levels were
determined.
[0400] The nucleotide sequence of AL-DUP 5167 is given above in
Table 10.
[0401] This experiment was undertaken to assess the dose response
for AL-DUP 5167.
[0402] At a dose of 100 mg/kg body weight, AL-DUP 5167 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 48.+-.13% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 37.+-.3% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 57.+-.14% of
carrier control levels. Serum cholesterol was lowered to 71.+-.14%
of carrier control levels.
[0403] At a dose of 50 mg/kg body weight, AL-DUP 5167 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 79.+-.15% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 67.+-.15% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 69.+-.17% of
carrier control levels. Serum cholesterol was found essentially
unchanged at 90.+-.28% of carrier control levels.
[0404] At a dose of 25 mg/kg body weight, AL-DUP 5167 was found to
leave the levels of ApoB mRNA present in samples of liver tissue
from treated mice essentially unchanged at 96.+-.7% of the mRNA
levels present in liver tissue of animals receiving carrier only,
and levels of ApoB mRNA in jejunum were lowered to 56.+-.11% of the
levels in control animals, as determined by the branched-DNA assay.
Serum ApoB protein concentration in mouse sera were determined to
68.+-.26% of carrier control levels. Serum cholesterol was found
essentially unchanged at 93.+-.8% of carrier control levels.
[0405] At a dose of 12.5 mg/kg body weight, AL-DUP 5167 was found
to leave the levels of ApoB mRNA present in samples of liver tissue
from treated mice essentially unchanged at 90.+-.14% of the mRNA
levels present in liver tissue of animals receiving carrier only,
and levels of ApoB mRNA in jejunum were unchanged at 77.+-.22% of
the levels in control animals, as determined by the branched-DNA
assay. Serum ApoB protein concentration in mouse sera were
determined to 95.+-.5% of carrier control levels. Serum cholesterol
was found essentially unchanged at 91.+-.14% of carrier control
levels.
[0406] I): 8 groups of 6 animals, age 2.5 months, received a single
intravenous bolus dose of 100 mg/kg body weight of AL-DUP 5167 (for
sequence, see Table 10), or an equivalent amount of carrier. Groups
of animals treated with AL-DUP 5167 were sacrificed 18 h, 66 h, 96
h, 168 h, and 336 h post-dosing; groups of animals treated with
carrier were sacrificed 18 h, 66 h, and 240 h post-dosing. The
group sacrificed after 240 h was used as the control, all values
are expressed as percent of the average found in this group. Total
serum cholesterol, serum ApoB 100 concentration, and liver and
jejunum ApoB mRNA levels were determined. An S1-nuclease protection
assay was used to determine the amounts of AL-DUP-5167 present in
liver tissues.
[0407] This experiment was designed to confirm the time course of
the effects of AL-DUP 5167 on ApoB mRNA levels in liver and
jejunum, and on serum ApoB and cholesterol concentrations, and to
extend the time of observation.
[0408] 18 h post-dosing, 3.3 .mu.g/g tissue of AL-DUP 5167 were
recovered in liver samples, which dropped to 22 ng/g tissue after
66 h, and below the limit of detection thereafter.
[0409] In animals sacrificed 18 hours post dosing of 100 mg/kg
AL-DUP 5167 intravenously, 37.+-.16% of the ApoB mRNA levels
present in liver tissue of the 240 h carrier control group were
found in the liver, and 87.+-.29% of the ApoB mRNA levels present
in jejunum tissue of the 240 h carrier control group were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to XX.+-.X % of carrier control levels.
[0410] In animals sacrificed 66 hours post dosing of 100 mg/kg
AL-DUP 5167 intravenously, 47.+-.7% of the ApoB mRNA levels present
in liver tissue of the 240 h carrier control group were found in
the liver, and 43.+-.8% of the ApoB mRNA levels present in jejunum
tissue of the 240 h carrier control group were found in the
jejunum. Serum ApoB protein concentration in mouse sera was lowered
to XX.+-.X % of carrier control levels.
[0411] In animals sacrificed 96 hours post dosing of 100 mg/kg
AL-DUP 5167 intravenously, 38.+-.9% of the ApoB mRNA levels present
in liver tissue of the 240 h carrier control group were found in
the liver, and 78.+-.14% of the ApoB mRNA levels present in jejunum
tissue of the 240 h carrier control group were found in the
jejunum.
[0412] Serum ApoB protein concentration in mouse sera was lowered
to XX.+-.X % of carrier control levels.
[0413] In animals sacrificed 168 hours post dosing of 100 mg/kg
AL-DUP 5167 intravenously, 57.+-.5% of the ApoB mRNA levels present
in liver tissue of the 240 h carrier control group were found in
the liver, and 87.+-.27% of the ApoB mRNA levels present in jejunum
tissue of the 240 h carrier control group were found in the
jejunum. Serum ApoB protein concentration in mouse sera was lowered
to XX.+-.X % of carrier control levels.
[0414] In animals sacrificed 336 hours post dosing of 100 mg/kg
AL-DUP 5167 intravenously, 94.+-.10% of the ApoB mRNA levels
present in liver tissue of the 240 h carrier control group were
found in the liver, and 109.+-.12% of the ApoB mRNA levels present
in jejunum tissue of the 240 h carrier control group were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to XX.+-.X % of carrier control levels.
[0415] In animals sacrificed 18 hours post dosing of saline control
AL-DUP 5167 intravenously, 83.+-.21% of the ApoB mRNA levels
present in liver tissue of the 240 h carrier control group were
found in the liver, and 109.+-.26% of the ApoB mRNA levels present
in jejunum tissue of the 240 h carrier control group were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to 51.+-.8% of carrier control levels.
[0416] In animals sacrificed 18 hours post dosing of 100 mg/kg
AL-DUP 5167 intravenously, 104.+-.19% of the ApoB mRNA levels
present in liver tissue of the 240 h carrier control group were
found in the liver, and 97.+-.21% of the ApoB mRNA levels present
in jejunum tissue of the 240 h carrier control group were found in
the jejunum. Serum ApoB protein concentration in mouse sera was
lowered to 51.+-.8% of carrier control levels.
[0417] This experiment shows that the action of a
cholesterol-conjugated siRNA may persist for 7 days or more in the
liver, and 3 days or more in the gut. The latter is consistent with
the average lifespan of the intestinal enterocyte.
[0418] Conclusions from experiments A)-I): An important
consideration for siRNA based inhibition to gene expression is
whether the observed effects are specific and not due to "off
target" effects and potential interferon responses that have been
reported with siRNAs in vitro and other oligonucleotide-based
approaches. In our experiments, the effects of ApoB-specific,
cholesterol-conjugated siRNAs were seen with several independent
siRNAs targeting separate sequence regions of the ApoB mRNA.
Further, the in vivo silencing of ApoB was specific as neither an
unspecific siRNA nor a mismatch control siRNA mediated a
significant reduction in ApoB mRNA, plasma ApoB protein levels, or
total cholesterol. Cholesterol-conjugated ApoB-specific siRNAs, but
not unconjugated ApoB-specific siRNAs, showed biological activity,
demonstrating an important role for cholesterol conjugation to
achieve systemic in vivo activity and suggesting the opportunity to
further optimize activity based on systemic administration through
chemical conjugation strategies.
Example 8
Cholesterol Stabilizes siRNA Activity
[0419] In exploring the potential for synthetic siRNAs to silence
endogenous target genes in vivo, we have found that
chemically-stabilized and cholesterol-conjugated siRNAs have
markedly improved pharmacologic properties in vitro and in vivo.
Chemically stabilized siRNAs with partial phosphorothioate backbone
and 2'-O-methyl modifications on the sense and antisense strands
showed significantly enhanced resistance towards degradation by
exo- and endonucleases in serum and tissue homogenates. The
conjugation of cholesterol at the 3'-end of the sense strand of a
siRNA via a pyrrolidine linker (thereby generating
cholesterol-conjugated siRNA) did not result in a significant loss
of gene silencing activity in cell culture. In HeLa cells
transiently expressing luciferase from a transfected plasmid and in
the absence of transfection reagent or electroporation only a
cholesterol-conjugated siRNA inhibited luciferase expression
(IC.sub.50 200 nM) whereas unconjugated siRNA was inactive. Binding
of cholesterol-conjugated siRNAs to human serum albumin (HSA) was
determined by surface plasmon resonance measurement; unconjugated
siRNAs demonstrated no measurable binding to HSA, while
cholesterol-conjugated siRNAs were found to bind to HSA with an
estimated K.sub.D=1 .mu.M. Due to enhanced binding to serum
proteins, cholesterol-conjugated siRNAs administered to rats by IV
injection showed improved in vivo pharmacokinetic properties as
compared to unconjugated siRNAs. Following IV injection in rats at
50 mg/kg, radioactively-labeled cholesterol-conjugated siRNAs had a
t.sub.1/2=95+/-13 min in plasma whereas unconjugated siRNAs had a
plasma t.sub.1/2=6.2+/-0.6 min, as determined by curve fitting
simulation assuming a two compartment model, first order
elimination rate, using WinNonLin 4.1 (Pharsight Corporation,
Mountain View, Calif., USA). As measured by RNase protection assay,
cholesterol-conjugated siRNAs showed broad tissue biodistribution
24 h after a single 50 mg/kg IV bolus injection in mice. Whereas no
detectable amounts of unconjugated siRNAs were observed in tissue
samples, significant levels of cholesterol-conjugated siRNAs of
about 200 ng/g tissue were detected in liver, heart, kidney, and
lung samples. Together, these studies demonstrated that cholesterol
conjugation significantly improves in vivo pharmacokinetic
properties of siRNAs.
Example 9
ApoB Expression in Human ApoB-100 Transgenic Mice is Reduced by
siRNAs Specific for Human and Mouse ApoB
[0420] The experimental procedures were approved by the Alnylam
Institutional Animal Care and Use Committee, and were performed in
accordance with city of Cambridge, Mass. regulations regarding
animal welfare.
[0421] Hemizygous male Human ApoB-100 transgenic mice (strain
designation: B6.5SJL-Tg(APOB100)N20) were obtained from Taconic
(Taconic, Germantown, N.Y., USA, cat. no. 1004-T) and were housed
at constant temperature and humidity on a 12 hr light/dark cycle
(6:30 AM/6:30 PM). Animals were fed irradiated standard rodent chow
(PicoLab.RTM. Rodent Diet 20, Purina Mills, LLC, St. Louis, Mo.,
USA, cat. no. 5053).
[0422] Animals at 30-32 weeks of age were divided into three groups
of eight for treatment. One group received three daily tail vein
injections (24 hours between doses) of phosphate buffered saline
(10 .mu.l per gram body weight). A second group received three
daily tail vein injections (24 hours between injections) of 50 mg
siRNA AL-DUP 5167 per kilogram body weight in a dosing volume of 10
.mu.l per gram body weight. The third group received three daily
tail vein injections (24 hours between injections) of 50 mg siRNA
AL-DUP 5311 per kilogram body weight in a dosing volume of 10 .mu.l
per gram body weight. The siRNA duplexes were formulated in
phosphate buffered saline.
[0423] Twenty-four hours after the final injection, animals were
sacrificed by CO.sub.2 asphyxiation. Whole liver as well as the
segment of the small intestine corresponding to the jejunum was
harvested from each animal and rapidly frozen in liquid nitrogen.
Frozen tissues were ground to a fine powder using a mortar and
pestle.
[0424] Approximately 10 mg of each tissue powder was added to an
ice-cold 1.5 ml Eppendorf tube, and 1 ml Tissue and Cell Lysis
Solution (Epicentre, Madison, Wis., USA, cat. No. MTC096H)
containing 3.3 .mu.l (10 .mu.l per 3 ml) of a 50 .mu.g/.mu.l stock
solution of Proteinase K (Epicentre, Madison, Wis., USA, cat. No.
MPRK092) were added. The tubes were vortexed and incubated at
65.degree. C. for 15 minutes; vortexing every 5 minutes. Cellular
debris was pelleted at 5000 rcf for 10 minutes at RT, and 800 .mu.l
supernatant were transferred to a fresh tube. Lysates were used
immediately in the branched DNA assay (described above) to
determine relative levels of ApoB and GAPDH mRNA, or stored at
-80.degree. C. for later use.
[0425] The ApoB specific siRNA AL-DUP 5167 was found to reduce
mouse ApoB mRNA levels (significantly different at p<0.01);
43.+-.10% in liver and 58.+-.12% in jejunum of mouse ApoB mRNA
levels in carrier treated animals were found in animals treated
with AL-DUP 5167. Human ApoB mRNA in liver was reduced to 40.+-.10%
of levels in livers of control animals. The mismatch control siRNA
AL-DUP 5311 was found to leave ApoB mRNA levels essentially
unchanged; 93.+-.20% in liver and 104.+-.13% in jejunum of mouse
ApoB mRNA levels in carrier treated animals were found in animals
treated with AL-DUP 5167. Human ApoB mRNA in liver was determined
to 92.+-.24% of levels in livers of control animals.
Example 10
Specific ApoB Cleavage Sites can be Identified by 5'-RACE PCR
[0426] Primers were purchased from Operon Biotechnologies, Inc.
(Alameda, Calif., USA).
[0427] The specific siRNA-induced cleavage products of ApoB mRNA in
pooled liver and jejunum from each of the treatment groups of
experiment (G.) above (Example 7) were identified by 5'-RACE as
described in Llave, et al. Science 2002, 297:2053-6, and Yekta, et
al. Science 2004, 304:594-6, with the following modifications and
primers given below. In such experiment, an adaptor is reacted with
5'-phosphate-bearing RNA present in an RNA sample, such as the
3'-products of the cleavage of mRNA by siRNA-complexed RISC. The
products of most, if not all, nucleolytic reactions catalyzed by
nucleases do not contain a 5'-phosphate group and therefore will
not react with the adaptor. In the subsequent PCR reactions, only
those molecular species comprising both the adaptor sequences as
well as the target gene sequence are amplified by appropriate
selection of primers.
[0428] Following ligation of the RACE adapter ("GeneRacer" adapter,
Invitrogen), cDNA synthesis was primed using a gene specific
primer, 5167GSP, to yield "5167" cDNA. Sequences corresponding to
ApoB were amplified in sequential PCR reactions using the following
primer pairs:
GR5'-XbaI(forward)+5167 ApoB Rev2-SalI(reverse) PCR reaction 1
GS5'Nest F-XbaI(forward)+5167 ApoB Rev3-SalI(reverse) PCR reaction
2
[0429] A fifty-fold dilution of PCR reaction 1 was used in PCR
reaction 2. Products of each PCR reaction were analyzed by agarose
gel electrophoresis, and visualized by ethidium bromide staining
Specific bands of the expected size corresponding to siRNA-directed
cleavage were seen in liver from animals receiving AL-DUP 5167 and
in jejunum from animals receiving AL-DUP 5167 and, to a lesser
extent, AL-DUP 5385 (see FIG. 7).
[0430] The specific bands from PCR reaction 1 were excised and
sequenced (sequencing primer: 5167 ApoB Rev3-SalI) to confirm the
presence of the junction between the RACE adapter and nucleotide
10226 of mouse ApoB (Accession number: XM137955).
[0431] To specifically amplify fragments corresponding to the
predicted siRNA cleavage site, PCR reaction 1 was diluted fifty
fold and amplified with the following primer pairs:
iApoB 5167-XbaI(forward)+5167 ApoB Rev3-SalI(reverse) PCR reaction
3
[0432] A PCR product is formed in PCR reaction 3 if and only if a
reaction product is present in PCR reaction 1 combining the RACE
adaptor with the RISC cleavage product of ApoB mRNA predicted by
RNA interference mediated by AL-DUP 5167. Products of this PCR
reaction were visualized as described above (FIG. 7). Confirmatory
sequencing of the amplified bands was performed as above.
[0433] Primer Sequences:
TABLE-US-00026 GR5'-XbaI SEQ. ID NO. 279 5'-
TCTAGAGCGACTGGAGCACGAGGACACTGA-3' GS5'Nest F-XbaI SEQ. ID NO. 280
5'- TCTAGAGGGACACTGACATGGACTGAAGGAGTA-3' 5167 GSP SEQ. ID NO. 281
5'- TCCTGTTGCAGTAGAGTGCAGCT-3' 5167 ApoB Rev2-Sal I SEQ.ID NO. 282
5'- CGCGTCGACGTGGGAGCATGGAGGTTGGCAGTTGTTC-3' 5167 ApoB Rev3-Sal I
SEQ. ID NO. 283 5'- CGCGTCGACGTAATGGTGCTGTCATGACTGCCCTT-3' iApoB
5167-Xba I SEQ. ID NO. 284 5'-
TCTAGAGCATGGACTGAAGGAGTAGAAAGAA-3'
Example 11
Further Testing of Modified siRNAs
[0434] Design of further modified siRNAs
[0435] Further siRNAs representing modified versions of AL-DUP
5002, AL-DUP 5035, AL-DUP 5048, AL-DUP 5089, AL-DUP 5097, and
AL-DUP 5098 were tested for stability and activity towards
inhibiting the expression of ApoB. A modified version of AL-DUP
5048 was synthesized bearing a cholesteryl moiety linked to the
3'-end of the sense strand via a pyrrolidine linker. For each of
the unmodified iRNA agents AL-DUP 5002, AL-DUP 5035, AL-DUP 5089,
AL-DUP 5097, and AL-DUP 5098, one iRNA agent was synthesized with a
21-nucleotide sense strand, a 23-nucleotide antisense strand
forming a 2-nucleotide 3'-overhang, bearing a cholesteryl moiety on
the 3'-end of the sense strand linked via a
phosphorothioate-comprising linker, 2'-O-methyl nucleotides in
positions 21 and 22 of the antisense strand, and phosphorothioate
linkages between positions 21 and 22, and 22 and 23, of the
antisense strand. This configuration corresponds to the pattern of
modifications already used in AL-DUP 5167, and is meant to protect
the iRNA agent from the degrading activity of exonucleases.
[0436] In addition, a second iRNA agent was synthesized
representing a modified version of AL-DUP 5002, AL-DUP 5035, AL-DUP
5089, AL-DUP 5097, and AL-DUP 5098, bearing a cholesteryl moiety on
the 3'-end of the sense strand linked via a
phosphorothioate-comprising linker, 2'-O-methyl modified
nucleotides in the positions of the 5'-most pyrimidines in all
occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3',
and 5'-UG-3', and phosphorothioate linkages between positions 21
and 22, and 22 and 23, of the antisense strand. These additional
modifications were made to protect these siRNAs from the degrading
activity of endonucleases. The corresponding sequences are listed
in Table 11.
TABLE-US-00027 TABLE 11 Modified iRNA agents for stability and
activity assays SEQ. SEQ. Duplex ID ID descriptor No. Sense strand
sequence No. Antisense strand sequence AL-DUP 5546 285
ucaucacacugaauaccaau(chol) 286 aggguugaagccauacaccumcmu AL-DUP 5536
287 aumumgaumumgaccumguccmaumuc(chol) 288
aaumggacmaggucaaucmaaucmumu AL-DUP 5537 289
auugauugaccuguccauuc(chol) 290 aauggacaggucaaucaaucmumu AL-DUP 5538
291 cmaccmaacumucumuccmacgaguc(chol) 292
gacucgumggaagaagumumggumgmumu AL-DUP 5539 293
caccaacuucuuccacgaguc(chol) 294 gacucguggaagaaguuggugmumu AL-DUP
5540 295 gagumumumgumgacmaaaumaumgggc(chol) 296
gcccmaumaumumumgucmacmaaacucmcma AL-DUP 5541 297
gaguuugugacaaauaugggc(chol) 264 gcccauauuugucacaaacucmcma AL-DUP
5542 262 cumumumacmaagccumumggumucmagu(chol) 263
acumgaaccmaaggcumumgumaaagmumg AL-DUP 5543 260
cuuuacaagccuugguucagu(chol) 259 acugaaccaaggcuuguaaagmumg AL-DUP
5544 258 ggaaucumumaumaumumumgauccmaa(chol) 257
umumggaucmaaaumaumaagaumuccmcmu AL-DUP 5545 252
ggaaucuuauauuugauccaa(chol) 251 uuggaucaaauauaagauuccmcmu m =
2'O-methyl modification; "(chol)" indicates cholesterol conjugated
to the 3'-end via a pyrrolidine linker comprising a
phosphorothioate; "(chol)" indicates cholesterol conjugated to the
3'-end via a pyrrolidine linker lacking a phosphorothioate
[0437] siRNA Stability Testing
[0438] The siRNAs, the sequences of which are shown in Table 11,
were tested for stability by incubation in human serum
(Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany, cat. No. H1513)
followed by isolation of separation of fragments by HPLC. A 50
.mu.M solution of the respective siRNA in phosphate buffered saline
(PBS, Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany) was
incubated with serum at a ratio of 10:1 serum:siRNA solution for 30
min, 1, 2, 4, 8, 16 and 24 hours, and samples were analysed as
described below.
[0439] Determination of siRNA degradation time course by HPLC
following Proteinase K treatment of serum samples
[0440] Proteinase K (20 mg/ml) was obtained from peQLab (Erlangen,
Germany; Cat.-No. 04-1075) and diluted 1:1 with deionized water
(18.2 m.OMEGA.) to a final concentration of 10 mg/ml Proteinase K.
Proteinase K Buffer (4.0 ml TRIS-HCl 1M pH 7.5, 1.0 ml EDTA 0.5M,
1.2 ml NaCl 5M, 4.0 ml SDS 10%) was prepared fresh and kept at
50.degree. C. until use to avoid precipitation.
[0441] A 40 mer of poly(L-dT), (L-dT).sub.40 was obtained from
Noxxon Pharma AG (Berlin, Germany) and used as an internal
standard. Polymers of the L-enantiomers of nucleic acids show an
extraordinary stability towards nucleolytic degradation (Klussman
S, et al., Nature Biotechn. 1996, 14:1112) but otherwise very
similar properties when compared to naturally occurring nucleic
acids consisting of R-enantiomers.
[0442] To terminate the siRNA-degradation, 25 .mu.l of Proteinase K
buffer were added to serum incubation samples immediately after
expiry of the respective incubation period, the mixture vortexed at
highest speed for 5 s (Vortex Genie 2, Scientific Industries, Inc.,
Bohemia, N.Y., USA, cat. no. S10256), 8 .mu.l Proteinase K (10
mg/ml) were added followed by vortexing for 5 s, and finally the
mixture was incubated for 20 min in a thermomixer at 42.degree. C.
and 1050 rpm.
[0443] 5 .mu.l of a 50 .mu.M solution (250 pmole) of (L-dT).sub.40
were added as an internal standard to each well, the solution was
vortexed for 5 s, and the tube centrifuged for 1 min in a tabletop
centrifuge to collect all droplets clinging to the inner surfaces
of the wells at the bottom. The solution was transferred to a 96
well Captiva 0.2 um filter plate (Varian, Germany, Cat. No.
A5960002) and filtered by centrifugation at 21900 rcf for 45
min.
[0444] The incubation wells were washed with 47.5 .mu.l deionized
water (18.2 ma), the wash filtered through the Captiva Filter Unit
at 21900 rcf for 15 min, and the wash step repeated. Approximately
180 .mu.l of the theoretical total volume of 200 .mu.l are on
average recovered after the second washing step.
[0445] Ion exchange chromatographic separation of siRNA single
strands from each other and from degradation products:
[0446] A Dionex BioLC HPLC-system equipped with inline-degasser,
autosampler, column oven and fixed wavelength UV-detector (Dionex
GmbH, Idstein, Germany) was used under denaturing conditions.
Standard run parameters were: [0447] Column: Dionex DNA-Pac100;
4.times.250 mm [0448] Temperature: 75.degree. C. [0449] Eluent A:
10 mM NaClO.sub.4, 20 mM TRIS-HCl, 1 mM EDTA; 10% acetonitrile,
pH=8.0 [0450] Eluent B: 800 mM NaClO.sub.4, 20 mM TRIS-HCl, 1 mM
EDTA; 10% acetonitrile, pH=8.0 [0451] Detection: @260 nm [0452]
Gradient: 0-1 min: 10% B [0453] 1-11 min: 10%->35% B [0454]
11-12 min: 35% B->100% B [0455] 12-14 min: 100% B->10% B
[0456] 14-16 min: 10% B for column reequilibration [0457] Injection
volume: 20 .mu.l
[0458] Where separation between the two strands of an siRNA was not
satisfactory or a degradation fragment co-eluted with one strand,
the chromatographic parameters were adjusted by changing
temperature, pH, replacement of NaClO.sub.4 by NaBr, the
concentration of acetonitrile, and/or adjusting the slope of the
eluent gradient until separation was achieved which allowed
separate quantitation of the peaks from sense and antisense
strand.
[0459] Peak areas for full length strands were obtained by
integration of the UV detector signal using software supplied by
the manufacturer of the instrument (Chromeleon 6.6; Dionex GmbH,
Idstein, Germany).
[0460] Data Analysis:
[0461] Integrated sense strand, antisense strand, and internal
standard peak areas were obtained for all samples and the
normalization control.
[0462] A correction factor CF, accounting for liquid losses in the
filtration and washing steps, was determined for every sample by
calculating the ratio of experimental to theoretical internal
standard peak area. The theoretical internal standard peak area is
obtained, e.g. from a calibration curve of the internal standard
obtained by injecting 50 .mu.l each of a serial dilution of the 50
.mu.M solution of (L-dT).sub.40 onto the HPLC column, and
calculation of the theoretical peak area corresponding to 25 pmole
(L-dT).sub.40 with the equation obtained by linear least square fit
to the peak areas from the dilution series. The correction factor
CF to be applied to the peak areas of the sense and antisense
strand is the obtained as:
CF=PeakArea.sub.intStd(theoretical)/PeakArea.sub.intStd(Sample)
[0463] This treatment assumes that, by virtue of washing the filter
twice, virtually complete recovery is achieved in the combined
filtrates, and corrects for the variable volume of wash water
retained in the filter, such that peak areas from different samples
can be compared.
[0464] The peak areas obtained for the sense and antisense strand
peaks for each time point are then multiplied with the correction
factor CF to obtain Normalized Peak Areas (NPA.sub.sense,t,
NPA.sub.antisense,t):
NPA.sub.sense or antisense,t=(Peak Area.sub.sense or
antisense,t).times.CF
[0465] To obtain the relative amount of remaining Full Length
Product (% FLP) for the sense and antisense strands at time t, the
Normalized Peak Area for each strand at time t=0 min
(NPA.sub.sense,t=.sub.0, NPA.sub.antisense,t=0) is set as 100%, and
the NPAs from other time points are divided by these values.
% FLP.sub.t=1,2,3 . . . n=(NPA.sub.t=1,2,3 . . .
n/NPA.sub.t=0)*100
[0466] The value obtained from the control sample, where the siRNA
was incubated with annealing buffer only, may serve as a control of
the accuracy of the method. The % FLP for both strands should lie
near 100%, within error margins, regardless of time of
incubation.
[0467] The degradation half life t.sub.1/2 may then be calculated
for each strand, assuming first order kinetics, from the slope of a
linear least square fit to a plot of ln(% FLP) versus time as:
t.sub.1/2=ln(0,5)/slope
[0468] Serum half lifes of siRNAs described by the sequences in
Table 11
[0469] The degradation half lifes of the full length products of
the siRNAs described by the sequences shown in Table 11 are given
in Table 12. As is evident from the difference in the half life of
the antisense strand of AL-DUP 5546 compared to the half life of
its sense strand or the antisense strand of AL-DUP 5167, protecting
the 3'-end of a strand by means of 2'-O-methyl groups and
phosphorothioate linkages in the 3'-penultimate nucleotides affords
an increase of approximately 6- to 7-fold in terms of the
degradation half life. Further substituting 2'-O-methyl modified
nucleotides at sites particularly prone to endonucleolytic
degradation further improved half lifes by approximately 3- to
4-fold, except for AL-DUP 5543, where the average-fold improvement
was 20.
TABLE-US-00028 TABLE 12 Serum half lifes of siRNAs with different
stabilizing modifications t.sub.1/2 t.sub.1/2 (sense strand)
(antisense strand) average-fold Duplex descriptor [h] [h]
improvement.sup.1 AL-DUP 5167 8.7 6.5 4 AL-DUP 5546 6.8 0.9 AL-DUP
5536 22.7 16.6 3 AL-DUP 5537 7.4 7.7 AL-DUP 5538 21.1 18.4 4 AL-DUP
5539 6.3 3.7 AL-DUP 5540 27.3 24.7 3 AL-DUP 5541 8.2 9.0 AL-DUP
5542 40.3 15.9 20 AL-DUP 5543 1.5 1.2 AL-DUP 5544 17.5 14.9 3
AL-DUP 5545 5.7 6.8 .sup.1[((t.sub.1/2(modified sense
strand)/t.sub.1/2(unmodified sense strand)) + (t.sub.1/2(modified
antisense strand)/t.sub.1/2(unmodified antisense strand)))/2]
[0470] In vitro activity of siRNAs modified to resist
endonucleolytic degradation
[0471] In vitro activity of the siRNAs of Table 11 was tested as
described in Example 3 hereinabove. Results are shown in Table
13.
TABLE-US-00029 TABLE 13 In vitro activity of siRNAs modified to
resist endonucleolytic degradation compared to IC.sub.50 modified
IC.sub.50 unmodified Duplex descriptor [nM] Duplex descriptor [nM]
AL-DUP 5167 0.4 AL-DUP 5546 0.5 AL-DUP 5536 0.6 AL-DUP 5537 0.6
AL-DUP 5538 21 AL-DUP 5539 1 AL-DUP 5540 7 AL-DUP 5541 7 AL-DUP
5542 3 AL-DUP 5543 6 AL-DUP 5544 7 AL-DUP 5545 4
[0472] As is evident from the comparison of the IC.sub.50 for
AL-DUP 5167 and AL-DUP 5546 in Table 13, the introduction of
phosphorothioate linkages between positions 21 and 22, and 22 and
23, and 2'-O-methyl groups in positions 21 and 22, of the antisense
strand, in AL-DUP 5167 did not adversely affect the activity of
this siRNA. Furthermore, as can be seen from a comparison of the
IC.sub.50 for AL DUP 5536 vs. AL-DUP 5537, AL DUP 5538 vs. AL DUP
5539. AL DUP 5540 vs. AL-DUP 5541, AL DUP 5542 vs. AL-DUP 5543, and
AL DUP 5544 vs. AL DUP 5545, the introduction of 2'-O-methyl
modified nucleotides in the positions of the 5'-most pyrimidines in
all occurrences of the sequence motifs 5'-UA-3', 5'-CA-3',
5'-UU-3', and 5'-UG-3' in most cases had no adverse impact on the
activity of these molecules either.
[0473] In vivo activity of siRNAs modified to resist
endonucleolytic degradation
[0474] The following experiment was performed using routines and
procedures as described in Example 7 above.
[0475] 13 groups of 5 animals, age 2.5 months, received a single
intravenous bolus dose of 100 mg/kg body weight of AL-DUP 5167, AL
DUP 5536, AL-DUP 5537, AL DUP 5538, AL DUP 5539, AL DUP 5540,
AL-DUP 5541, AL DUP 5542, AL-DUP 5543, AL DUP 5544, AL DUP 5545, or
an equivalent amount of carrier. Animals were sacrificed 72 h
post-dosing. Total serum cholesterol, serum ApoB 100 concentration,
and liver and jejunum ApoB mRNA levels were determined. In
addition, the concentration of the siRNA was determined in liver,
jejunum, and serum samples from 3 animals from each group by the
S1-nuclease protection assay as described in Example 7; however,
quantitation of radioactive band intensity was performed by visual
comparison of bands to the dilution series, and standard deviations
were not calculated.
[0476] The nucleotide sequence of AL-DUP 5167 is given above in
Table 10. The nucleotide sequences of AL DUP 5536, AL-DUP 5537, AL
DUP 5538, AL DUP 5539, AL DUP 5540, AL-DUP 5541, AL DUP 5542,
AL-DUP 5543, AL DUP 5544, and AL DUP 5545 are given above in Table
11.
[0477] This experiment was undertaken to assess the impact of
modifications introduced into siRNAs to improve their stability in
biological media on their gene expression inhibiting activity in
vivo.
[0478] At a dose of 100 mg/kg body weight, AL-DUP 5167 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 42.+-.12% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 45.+-.8% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 44.+-.23% of
carrier control levels. Serum cholesterol was left essentially
unchanged at 75.+-.20% of carrier control levels. Average iRNA
concentrations for 3 animals were found as approximately: liver, 70
ng/g, jejunum 14 ng/g, serum 14 ng/g.
[0479] At a dose of 100 mg/kg body weight, AL-DUP 5546 was found to
leave the levels of ApoB mRNA present in samples of liver tissue
from treated mice essentially unchanged at 95.+-.9% of the mRNA
levels present in liver tissue of animals receiving carrier only,
and levels of ApoB mRNA in jejunum were at 102.+-.16% of the levels
in control animals, as determined by the branched-DNA assay. Serum
ApoB protein concentration in mouse sera was left essentially
unchanged at 113.+-.39% of carrier control levels. Serum
cholesterol was elevated to 132.+-.10% of carrier control levels.
Average iRNA concentrations for 3 animals were found as
approximately: liver, 1 ng/g; jejunum, not detectable; serum, not
detectable.
[0480] At a dose of 100 mg/kg body weight, AL-DUP 5536 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 56.+-.8% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 28.+-.8% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 46.+-.6% of
carrier control levels. Serum cholesterol was lowered to 74.+-.33%
of carrier control levels. Average iRNA concentrations for 3
animals were found as approximately: liver, 2 ng/g; jejunum, 6
ng/g, serum, 6 ng/g.
[0481] At a dose of 100 mg/kg body weight, AL-DUP 5537 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 72.+-.11% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were essentially unchanged at 94.+-.9% of the levels in
control animals, as determined by the branched-DNA assay. Serum
ApoB protein concentration in mouse sera was left essentially
unchanged at 75.+-.25% of carrier control levels. Serum cholesterol
was left essentially unchanged at 118.+-.9% of carrier control
levels. Average iRNA concentrations for 3 animals were found as
approximately: liver, not detectable; jejunum, not detectable,
serum, 1 ng/g.
[0482] At a dose of 100 mg/kg body weight, AL-DUP 5538 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 56.+-.16% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 75.+-.1% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was left essentially unchanged
at 102.+-.27% of carrier control levels. Serum cholesterol left
essentially unchanged at 117.+-.18% of carrier control levels.
Average iRNA concentrations for 3 animals were found as
approximately: liver, 35 ng/g; jejunum, 7 ng/g, serum, 18 ng/g.
[0483] At a dose of 100 mg/kg body weight, AL-DUP 5539 was found to
leave the levels of ApoB mRNA present in samples of liver tissue
from treated mice essentially unchanged at 76.+-.18% of the mRNA
levels present in liver tissue of animals receiving carrier only,
and levels of ApoB mRNA in jejunum were lowered to 62.+-.12% of the
levels in control animals, as determined by the branched-DNA assay.
Serum ApoB protein concentration in mouse sera was left essentially
unchanged at 108.+-.23% of carrier control levels. Serum
cholesterol was left essentially unchanged at 102.+-.18% of carrier
control levels. Average iRNA concentrations for 3 animals were
found as approximately: liver, 7 ng/g; jejunum, 4 ng/g, serum, 2
ng/g.
[0484] At a dose of 100 mg/kg body weight, AL-DUP 5540 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 54.+-.12% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 54.+-.12% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was left essentially unchanged
at 72.+-.30% of carrier control levels. Serum cholesterol was left
essentially unchanged at 91.+-.10% of carrier control levels.
Average iRNA concentrations for 3 animals were found as
approximately: liver, 130 ng/g; jejunum, 28 ng/g, serum, 25
ng/g.
[0485] At a dose of 100 mg/kg body weight, AL-DUP 5541 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 73.+-.10% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 68.+-.5% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was left essentially unchanged
at 90.+-.8% of carrier control levels. Serum cholesterol was left
essentially unchanged at 99.+-.8% of carrier control levels.
Average iRNA concentrations for 3 animals were found as
approximately: liver, 72 ng/g; jejunum, 10 ng/g, serum, 7 ng/g.
[0486] At a dose of 100 mg/kg body weight, AL-DUP 5542 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 58.+-.9% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 28.+-.4% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 55.+-.9% of
carrier control levels. Serum cholesterol was left essentially
unchanged at 61.+-.27% of carrier control levels. Average iRNA
concentrations for 3 animals were found as approximately: liver, 8
ng/g; jejunum, 17 ng/g, serum, 22 ng/g.
[0487] At a dose of 100 mg/kg body weight, AL-DUP 5543 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 77.+-.5% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were essentially unchanged at 91.+-.14% of the levels in
control animals, as determined by the branched-DNA assay. Serum
ApoB protein concentration in mouse sera was left essentially
unchanged at 97.+-.16% of carrier control levels. Serum cholesterol
was left essentially unchanged at 128.+-.24% of carrier control
levels. Average iRNA concentrations for 3 animals were found as
approximately: liver, not detectable; jejunum, not detectable,
serum, not detectable.
[0488] At a dose of 100 mg/kg body weight, AL-DUP 5544 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 63.+-.6% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 20.+-.3% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 46.+-.5% of
carrier control levels. Serum cholesterol was lowered to 55.+-.5%
of carrier control levels. Average iRNA concentrations for 3
animals were found as approximately: liver, >900 ng/g; jejunum,
60 ng/g, serum, 40 ng/g.
[0489] At a dose of 100 mg/kg body weight, AL-DUP 5545 was found to
lower the levels of ApoB mRNA present in samples of liver tissue
from treated mice to 58.+-.11% of the mRNA levels present in liver
tissue of animals receiving carrier only, and levels of ApoB mRNA
in jejunum were lowered to 37.+-.11% of the levels in control
animals, as determined by the branched-DNA assay. Serum ApoB
protein concentration in mouse sera was lowered to 50.+-.6% of
carrier control levels. Serum cholesterol was left essentially
unchanged at 75.+-.28% of carrier control levels. Average iRNA
concentrations for 3 animals were found as approximately: liver, 70
ng/g; jejunum, 7 ng/g, serum, not detectable.
Example 12
Testing siRNAs for Immunogenic Potential
[0490] Recently, several reports have been published that
postulated a potential of siRNA agents to illicit a possibly
adverse immunogenic response (see, for example, Hornung et al.,
Nature Med 2005, 11:263-270). Little is known about the biological
consequences of, for example, a temporary interferon-.alpha.
(IFN-.alpha.) increase in humans potentially caused by siRNA. To
circumvent unnecessary, hazardous side effects, it is desirable to
have a potent antiviral siRNA with little or no detectable
immunostimulatory activity. Albeit a true simulation of the exact
processes in humans are not possible, we consider the described
experiment as appropriate for predicting immunostimulation by
oligonucleotides and siRNA.
[0491] We tested the immunogenicity of the siRNAs listed in Table
11 by measuring the induction of IFN-.alpha. in peripheral blood
mononuclear cells (PBMC) by siRNAs AL-DUP 5167, AL-DUP 5536, AL-DUP
5537, AL DUP 5538, AL DUP 5539, AL DUP 5542, AL-DUP 5543, AL DUP
5544, and AL DUP 5545. AL-DUP 5311 was included as an unrelated
sequence control. ODN2216, a strong inducer of IFN-.alpha. (Hornung
et al., Nature Med 2005, 11:263-270) was used as a positive
control, PBS as negatice control. The nucleotide sequence of
ODN2216 is
TABLE-US-00030 SEQ. ID NO. 306 5'- GGGGACGATCGTCGGGGGG-3'
[0492] PBMC were isolated by Ficoll gradient centrifugation as
described in Chang, H. S., and Sack, D. A., Clin. Diag. Lab.
Immunology 2001, 8: 482-488, except that an unfiltered, erythrocyte
depleted leukocyte concentrate (Buffy Coat) from single donors
obtained from the Institute for Transfusion Medicine gGmbH, Suhl,
Germany, diluted 1:1 with PBS, was employed as starting material,
and that the final suspension in RPMI complete medium (RPMI1640
complete; 10% FCS; 1% L-Glu) was adjusted to 1.times.10.sup.6
cells/ml.
[0493] Cells were incubated with ODN2216 or siRNAs in Opti-MEM or
Opti-MEM plus the transfection reagent GenPorter 2 (GP2; Peqlab
Biotechnologie GmbH, Erlangen, Germany). 100 .mu.l cell suspension
(100.000 cells) per well of a 96 well plate were combined with 50
.mu.l of a 1.5 .mu.M solution of oligonucleotide in Opti-MEM (final
oligonucleotide conc. 500 nM), or 50 .mu.l of a 1:1 mixture of a) a
mixture of 6 .mu.l of GP2 reagent with 119 .mu.l Opti-MEM, and b) a
mixture of 1 .mu.l 100 .mu.M solution of oligonucleotide in PBS and
124 .mu.l Diluent B from the GP2 kit (final oligonucleotide conc.
133 nM). The incubation was kept at 37.degree. C. for 24 h, and 50
.mu.l supernatant were carefully removed from the top of the well.
These were employed for IFN-.alpha. determination using the
huIFN-.alpha. instant ELISA (BenderMed Systems, Vienna, Austria,
catalogue no. BMS2161NST). Table 14 summarizes the results.
TABLE-US-00031 TABLE 14 IFN-.alpha. production by peripheral blood
mononuclear cells incubated with siRNAs or ODN2216 Duplex
descriptor IFN-.alpha. [pg/ml supernatant] Saline 0 .+-. 3 ODN 2216
383 .+-. 62 AL-DUP 5311 77 .+-. 4 AL-DUP 5167 193 .+-. 9 AL-DUP
5546 159 .+-. 33 AL-DUP 5536 0 .+-. 1 AL-DUP 5537 2 .+-. 1 AL-DUP
5538 -5 .+-. 0 AL-DUP 5539 -10 .+-. 1 AL-DUP 5542 -3 .+-. 1 AL-DUP
5543 -2 .+-. 0 AL-DUP 5544 -2 .+-. 0 AL-DUP 5545 -10 .+-. 0
[0494] Conclusions from Examples 11 and 12:
[0495] a) Oligonucleotides with modified nucleotides in certain
particularly degradation-prone sites benefit in terms of in vitro
half life in biological media while their in vitro and in vivo gene
expression inhibiting activity is largely unaffected
[0496] b) Depending on their sequence, siRNAs can be, but are not
generally, immunostimulatory agents.
[0497] c) AL-DUP 5536, AL-DUP 5540 and AL-DUP 5542 are particularly
promising candidates as iRNA agents for the inhibition of apoB
expression, and therefore as therapeutics for disorders involving
aberrant expression of apoB.
[0498] Table 15 lists the agent numbers that may be used herein to
designate the iRNA agents described above:
TABLE-US-00032 TABLE 15 IFN-.alpha. production by peripheral blood
mononuclear cells incubated with siRNAs or ODN2216 Duplex
descriptor Agent number AL-DUP 5163 54 AL-DUP 5164 55 AL-DUP 5165
56 AL-DUP 5166 57 AL-DUP 5167 58 AL-DUP 5168 59 AL-DUP 5169 60
AL-DUP 5170 61 AL-DUP 5180 62 AL-DUP 5181 63 AL-DUP 5182 64 AL-DUP
5183 65 AL-DUP 5536 66 AL-DUP 5537 67 AL-DUP 5538 68 AL-DUP 5539 69
AL-DUP 5542 70 AL-DUP 5543 71 AL-DUP 5544 72 AL-DUP 5545 73 AL-DUP
5545 74
Other Embodiments
[0499] A number of embodiments of the invention have been
described. Nevertheless, it will be understood that various
modifications may be made without departing from the spirit and
scope of the invention.
Sequence CWU 1
1
297121RNAArtificial SequenceSynthetically generated oligonucleotide
1aagccuuggu ucagugugga c 21223RNAArtificial SequenceSynthetically
generated oligonucleotide 2guccacacug aaccaaggcu ugu
23321RNAArtificial SequenceSynthetically generated oligonucleotide
3ugaacaccaa cuucuuccac g 21423RNAArtificial SequenceSynthetically
generated oligonucleotide 4cguggaagaa guugguguuc auc
23521RNAArtificial SequenceSynthetically generated oligonucleotide
5gauugauuga ccuguccauu c 21623RNAArtificial SequenceSynthetically
generated oligonucleotide 6gaauggacag gucaaucaau cuu
23721RNAArtificial SequenceSynthetically generated oligonucleotide
7aauggacuca ucugcuacag c 21823RNAArtificial SequenceSynthetically
generated oligonucleotide 8gcuguagcag augaguccau uug
23921RNAArtificial SequenceSynthetically generated oligonucleotide
9auugaccugu ccauucaaaa c 211023RNAArtificial SequenceSynthetically
generated oligonucleotide 10guuuugaaug gacaggucaa uca
231121RNAArtificial SequenceSynthetically generated oligonucleotide
11uuugugacaa auaugggcau c 211223RNAArtificial SequenceSynthetically
generated oligonucleotide 12gaugcccaua uuugucacaa acu
231321RNAArtificial SequenceSynthetically generated oligonucleotide
13cuugguucag uguggacagc c 211423RNAArtificial SequenceSynthetically
generated oligonucleotide 14ggcuguccac acugaaccaa ggc
231521RNAArtificial SequenceSynthetically generated oligonucleotide
15uggacucauc ugcuacagcu u 211623RNAArtificial SequenceSynthetically
generated oligonucleotide 16aagcuguagc agaugagucc auu
231721RNAArtificial SequenceSynthetically generated oligonucleotide
17auugauugac cuguccauuc a 211823RNAArtificial SequenceSynthetically
generated oligonucleotide 18ugaauggaca ggucaaucaa ucu
231921RNAArtificial SequenceSynthetically generated oligonucleotide
19uugauugacc uguccauuca a 212023RNAArtificial SequenceSynthetically
generated oligonucleotide 20uugaauggac aggucaauca auc
232121RNAArtificial SequenceSynthetically generated oligonucleotide
21caaauggacu caucugcuac a 212223RNAArtificial SequenceSynthetically
generated oligonucleotide 22uguagcagau gaguccauuu gga
232321RNAArtificial SequenceSynthetically generated oligonucleotide
23gauugaccug uccauucaaa a 212423RNAArtificial SequenceSynthetically
generated oligonucleotide 24uuuugaaugg acaggucaau caa
232521RNAArtificial SequenceSynthetically generated oligonucleotide
25ugauugaccu guccauucaa a 212623RNAArtificial SequenceSynthetically
generated oligonucleotide 26uuugaaugga caggucaauc aau
232721RNAArtificial SequenceSynthetically generated oligonucleotide
27gguguauggc uucaacccug a 212823RNAArtificial SequenceSynthetically
generated oligonucleotide 28ucaggguuga agccauacac cuc
232921RNAArtificial SequenceSynthetically generated oligonucleotide
29ucugugggau uccaucugcc a 213023RNAArtificial SequenceSynthetically
generated oligonucleotide 30uggcagaugg aaucccacag acu
233121RNAArtificial SequenceSynthetically generated oligonucleotide
31agacuuccug aauaacuaug c 213223RNAArtificial SequenceSynthetically
generated oligonucleotide 32gcauaguuau ucaggaaguc uau
233321RNAArtificial SequenceSynthetically generated oligonucleotide
33acaauuugau caguauauua a 213423RNAArtificial SequenceSynthetically
generated oligonucleotide 34uuaauauacu gaucaaauug uau
233521RNAArtificial SequenceSynthetically generated oligonucleotide
35ggacucaucu gcuacagcuu a 213623RNAArtificial SequenceSynthetically
generated oligonucleotide 36uaagcuguag cagaugaguc cau
233721RNAArtificial SequenceSynthetically generated oligonucleotide
37uuacuccaac gccagcucca c 213823RNAArtificial SequenceSynthetically
generated oligonucleotide 38guggagcugg cguuggagua agc
233921RNAArtificial SequenceSynthetically generated oligonucleotide
39gugacaaaua ugggcaucau c 214023RNAArtificial SequenceSynthetically
generated oligonucleotide 40gaugaugccc auauuuguca caa
234121RNAArtificial SequenceSynthetically generated oligonucleotide
41guguauggcu ucaacccuga g 214223RNAArtificial SequenceSynthetically
generated oligonucleotide 42cucaggguug aagccauaca ccu
234321RNAArtificial SequenceSynthetically generated oligonucleotide
43uaccguguau ggaaacugcu c 214423RNAArtificial SequenceSynthetically
generated oligonucleotide 44gagcaguuuc cauacacggu auc
234521RNAArtificial SequenceSynthetically generated oligonucleotide
45gauaccgugu auggaaacug c 214623RNAArtificial SequenceSynthetically
generated oligonucleotide 46gcaguuucca uacacgguau cca
234721RNAArtificial SequenceSynthetically generated oligonucleotide
47aaaucaagug ucaucacacu g 214823RNAArtificial SequenceSynthetically
generated oligonucleotide 48cagugugaug acacuugauu uaa
234921RNAArtificial SequenceSynthetically generated oligonucleotide
49agguguaugg cuucaacccu g 215023RNAArtificial SequenceSynthetically
generated oligonucleotide 50caggguugaa gccauacacc ucu
235121RNAArtificial SequenceSynthetically generated oligonucleotide
51guuugugaca aauaugggca u 215223RNAArtificial SequenceSynthetically
generated oligonucleotide 52augcccauau uugucacaaa cuc
235321RNAArtificial SequenceSynthetically generated oligonucleotide
53auaccgugua uggaaacugc u 215423RNAArtificial SequenceSynthetically
generated oligonucleotide 54agcaguuucc auacacggua ucc
235521RNAArtificial SequenceSynthetically generated oligonucleotide
55uaaaucaagu gucaucacac u 215623RNAArtificial SequenceSynthetically
generated oligonucleotide 56agugugauga cacuugauuu aaa
235721RNAArtificial SequenceSynthetically generated oligonucleotide
57gagguguaug gcuucaaccc u 215823RNAArtificial SequenceSynthetically
generated oligonucleotide 58aggguugaag ccauacaccu cuu
235921RNAArtificial SequenceSynthetically generated oligonucleotide
59uggcuucaac ccugagggca a 216023RNAArtificial SequenceSynthetically
generated oligonucleotide 60uugcccucag gguugaagcc aua
236121RNAArtificial SequenceSynthetically generated oligonucleotide
61gaacaccaac uucuuccacg a 216223RNAArtificial SequenceSynthetically
generated oligonucleotide 62ucguggaaga aguugguguu cau
236321RNAArtificial SequenceSynthetically generated oligonucleotide
63guauggcuuc aacccugagg g 216423RNAArtificial SequenceSynthetically
generated oligonucleotide 64cccucagggu ugaagccaua cac
236521RNAArtificial SequenceSynthetically generated oligonucleotide
65auggcuucaa cccugagggc a 216623RNAArtificial SequenceSynthetically
generated oligonucleotide 66ugcccucagg guugaagcca uac
236721RNAArtificial SequenceSynthetically generated oligonucleotide
67aacaccaacu ucuuccacga g 216823RNAArtificial SequenceSynthetically
generated oligonucleotide 68cucguggaag aaguuggugu uca
236921RNAArtificial SequenceSynthetically generated oligonucleotide
69acaccaacuu cuuccacgag u 217023RNAArtificial SequenceSynthetically
generated oligonucleotide 70acucguggaa gaaguuggug uuc
237121RNAArtificial SequenceSynthetically generated oligonucleotide
71caccaacuuc uuccacgagu c 217223RNAArtificial SequenceSynthetically
generated oligonucleotide 72gacucgugga agaaguuggu guu
237321RNAArtificial SequenceSynthetically generated oligonucleotide
73gaugaacacc aacuucuucc a 217423RNAArtificial SequenceSynthetically
generated oligonucleotide 74uggaagaagu ugguguucau cug
237521RNAArtificial SequenceSynthetically generated oligonucleotide
75augaacacca acuucuucca c 217623RNAArtificial SequenceSynthetically
generated oligonucleotide 76guggaagaag uugguguuca ucu
237721RNAArtificial SequenceSynthetically generated oligonucleotide
77agaugaacac caacuucuuc c 217823RNAArtificial SequenceSynthetically
generated oligonucleotide 78ggaagaaguu gguguucauc ugg
237921RNAArtificial SequenceSynthetically generated oligonucleotide
79auuccaucug ccaucucgag a 218023RNAArtificial SequenceSynthetically
generated oligonucleotide 80ucucgagaug gcagauggaa ucc
238121RNAArtificial SequenceSynthetically generated oligonucleotide
81uuccaucugc caucucgaga g 218223RNAArtificial SequenceSynthetically
generated oligonucleotide 82cucucgagau ggcagaugga auc
238321RNAArtificial SequenceSynthetically generated oligonucleotide
83acaagccuug guucagugug g 218423RNAArtificial SequenceSynthetically
generated oligonucleotide 84ccacacugaa ccaaggcuug uaa
238521RNAArtificial SequenceSynthetically generated oligonucleotide
85uucaagucug ugggauucca u 218623RNAArtificial SequenceSynthetically
generated oligonucleotide 86auggaauccc acagacuuga agu
238721RNAArtificial SequenceSynthetically generated oligonucleotide
87aaucaagugu caucacacug a 218823RNAArtificial SequenceSynthetically
generated oligonucleotide 88ucagugugau gacacuugau uua
238921RNAArtificial SequenceSynthetically generated oligonucleotide
89uauggcuuca acccugaggg c 219023RNAArtificial SequenceSynthetically
generated oligonucleotide 90gcccucaggg uugaagccau aca
239121RNAArtificial SequenceSynthetically generated oligonucleotide
91uugaccuguc cauucaaaac u 219223RNAArtificial SequenceSynthetically
generated oligonucleotide 92aguuuugaau ggacagguca auc
239321RNAArtificial SequenceSynthetically generated oligonucleotide
93aucaaguguc aucacacuga a 219423RNAArtificial SequenceSynthetically
generated oligonucleotide 94uucaguguga ugacacuuga uuu
239521RNAArtificial SequenceSynthetically generated oligonucleotide
95ucaaguguca ucacacugaa u 219623RNAArtificial SequenceSynthetically
generated oligonucleotide 96auucagugug augacacuug auu
239721RNAArtificial SequenceSynthetically generated oligonucleotide
97gucaucacac ugaauaccaa u 219823RNAArtificial SequenceSynthetically
generated oligonucleotide 98auugguauuc agugugauga cac
239921RNAArtificial SequenceSynthetically generated oligonucleotide
99cuguccauuc aaaacuacca c 2110023RNAArtificial
SequenceSynthetically generated oligonucleotide 100gugguaguuu
ugaauggaca ggu 2310121RNAArtificial SequenceSynthetically generated
oligonucleotide 101ccuguccauu caaaacuacc a 2110223RNAArtificial
SequenceSynthetically generated oligonucleotide 102ugguaguuuu
gaauggacag guc 2310321RNAArtificial SequenceSynthetically generated
oligonucleotide 103aucacacuga auaccaaugc u 2110423RNAArtificial
SequenceSynthetically generated oligonucleotide 104agcauuggua
uucaguguga uga 2310521RNAArtificial SequenceSynthetically generated
oligonucleotide 105accuguccau ucaaaacuac c 2110623RNAArtificial
SequenceSynthetically generated oligonucleotide 106gguaguuuug
aauggacagg uca 2310721RNAArtificial SequenceSynthetically generated
oligonucleotide 107gaccugucca uucaaaacua c 2110823RNAArtificial
SequenceSynthetically generated oligonucleotide 108guaguuuuga
auggacaggu caa 2310921RNAArtificial SequenceSynthetically generated
oligonucleotide 109caucacacug aauaccaaug c 2111023RNAArtificial
SequenceSynthetically generated oligonucleotide 110gcauugguau
ucagugugau gac 2311121RNAArtificial SequenceSynthetically generated
oligonucleotide 111uacaagccuu gguucagugu g 2111223RNAArtificial
SequenceSynthetically generated oligonucleotide 112cacacugaac
caaggcuugu aaa 2311321RNAArtificial SequenceSynthetically generated
oligonucleotide 113uguauggcuu caacccugag g 2111423RNAArtificial
SequenceSynthetically generated oligonucleotide 114ccucaggguu
gaagccauac acc 2311521RNAArtificial SequenceSynthetically generated
oligonucleotide 115ugaccugucc auucaaaacu a 2111623RNAArtificial
SequenceSynthetically generated oligonucleotide 116uaguuuugaa
uggacagguc aau 2311721RNAArtificial SequenceSynthetically generated
oligonucleotide 117ucaucacacu gaauaccaau g 2111823RNAArtificial
SequenceSynthetically generated oligonucleotide 118cauugguauu
cagugugaug aca 2311921RNAArtificial SequenceSynthetically generated
oligonucleotide 119uugugacaaa uaugggcauc a 2112023RNAArtificial
SequenceSynthetically generated oligonucleotide 120ugaugcccau
auuugucaca aac 2312121RNAArtificial SequenceSynthetically generated
oligonucleotide 121caagugucau cacacugaau a 2112223RNAArtificial
SequenceSynthetically generated oligonucleotide 122uauucagugu
gaugacacuu gau 2312321RNAArtificial SequenceSynthetically generated
oligonucleotide 123uaacacuaag aaccagaaga u 2112423RNAArtificial
SequenceSynthetically generated oligonucleotide 124aucuucuggu
ucuuaguguu agc 2312521RNAArtificial SequenceSynthetically generated
oligonucleotide 125caauuugauc aguauauuaa a 2112623RNAArtificial
SequenceSynthetically generated oligonucleotide
126uuuaauauac ugaucaaauu gua 2312721RNAArtificial
SequenceSynthetically generated oligonucleotide 127cugaacauca
agaggggcau c 2112823RNAArtificial SequenceSynthetically generated
oligonucleotide 128gaugccccuc uugauguuca gga 2312921RNAArtificial
SequenceSynthetically generated oligonucleotide 129ugaacaucaa
gaggggcauc a 2113023RNAArtificial SequenceSynthetically generated
oligonucleotide 130ugaugccccu cuugauguuc agg 2313121RNAArtificial
SequenceSynthetically generated oligonucleotide 131guccagcccc
aucacuuuac a 2113223RNAArtificial SequenceSynthetically generated
oligonucleotide 132uguaaaguga uggggcugga cac 2313321RNAArtificial
SequenceSynthetically generated oligonucleotide 133cagccccauc
acuuuacaag c 2113423RNAArtificial SequenceSynthetically generated
oligonucleotide 134gcuuguaaag ugauggggcu gga 2313521RNAArtificial
SequenceSynthetically generated oligonucleotide 135agccccauca
cuuuacaagc c 2113623RNAArtificial SequenceSynthetically generated
oligonucleotide 136ggcuuguaaa gugauggggc ugg 2313721RNAArtificial
SequenceSynthetically generated oligonucleotide 137gaguuuguga
caaauauggg c 2113823RNAArtificial SequenceSynthetically generated
oligonucleotide 138gcccauauuu gucacaaacu cca 2313921RNAArtificial
SequenceSynthetically generated oligonucleotide 139agggaaucuu
auauuugauc c 2114023RNAArtificial SequenceSynthetically generated
oligonucleotide 140ggaucaaaua uaagauuccc uuc 2314121RNAArtificial
SequenceSynthetically generated oligonucleotide 141uuacugagcu
gagaggccuc a 2114223RNAArtificial SequenceSynthetically generated
oligonucleotide 142ugaggccucu cagcucagua acc 2314321RNAArtificial
SequenceSynthetically generated oligonucleotide 143auugggaaga
agaggcagcu u 2114423RNAArtificial SequenceSynthetically generated
oligonucleotide 144aagcugccuc uucuucccaa uua 2314521RNAArtificial
SequenceSynthetically generated oligonucleotide 145ucacauccuc
caguggcuga a 2114623RNAArtificial SequenceSynthetically generated
oligonucleotide 146uucagccacu ggaggaugug agu 2314721RNAArtificial
SequenceSynthetically generated oligonucleotide 147gccccaucac
uuuacaagcc u 2114823RNAArtificial SequenceSynthetically generated
oligonucleotide 148aggcuuguaa agugaugggg cug 2314921RNAArtificial
SequenceSynthetically generated oligonucleotide 149ccagccccau
cacuuuacaa g 2115023RNAArtificial SequenceSynthetically generated
oligonucleotide 150cuuguaaagu gauggggcug gac 2315121RNAArtificial
SequenceSynthetically generated oligonucleotide 151aagggaaucu
uauauuugau c 2115223RNAArtificial SequenceSynthetically generated
oligonucleotide 152gaucaaauau aagauucccu ucu 2315321RNAArtificial
SequenceSynthetically generated oligonucleotide 153cuuuacaagc
cuugguucag u 2115423RNAArtificial SequenceSynthetically generated
oligonucleotide 154acugaaccaa ggcuuguaaa gug 2315521RNAArtificial
SequenceSynthetically generated oligonucleotide 155ggaaucuuau
auuugaucca a 2115623RNAArtificial SequenceSynthetically generated
oligonucleotide 156uuggaucaaa uauaagauuc ccu 2315721RNAArtificial
SequenceSynthetically generated oligonucleotide 157gaagggaauc
uuauauuuga u 2115823RNAArtificial SequenceSynthetically generated
oligonucleotide 158aucaaauaua agauucccuu cua 2315921RNAArtificial
SequenceSynthetically generated oligonucleotide 159aaauagaagg
gaaucuuaua u 2116023RNAArtificial SequenceSynthetically generated
oligonucleotide 160auauaagauu cccuucuauu uug 2316121RNAArtificial
SequenceSynthetically generated oligonucleotide 161uagaagggaa
ucuuauauuu g 2116223RNAArtificial SequenceSynthetically generated
oligonucleotide 162caaauauaag auucccuucu auu 2316321RNAArtificial
SequenceSynthetically generated oligonucleotide 163gacuuccuga
auaacuaugc a 2116423RNAArtificial SequenceSynthetically generated
oligonucleotide 164ugcauaguua uucaggaagu cua 2316521RNAArtificial
SequenceSynthetically generated oligonucleotide 165gcaaggaucu
ggagaaacaa c 2116623RNAArtificial SequenceSynthetically generated
oligonucleotide 166guuguuucuc cagauccuug cac 2316721RNAArtificial
SequenceSynthetically generated oligonucleotide 167caaggaucug
gagaaacaac a 2116823RNAArtificial SequenceSynthetically generated
oligonucleotide 168uguuguuucu ccagauccuu gca 2316921RNAArtificial
SequenceSynthetically generated oligonucleotide 169acggcuagcu
gugaaagguc c 2117023RNAArtificial SequenceSynthetically generated
oligonucleotide 170ggaccuuuca cagcuagccg uga 2317121RNAArtificial
SequenceSynthetically generated oligonucleotide 171ccacaugaag
cagcacgacu n 2117220RNAArtificial SequenceSynthetically generated
oligonucleotide 172aagucgugcu gcuucaugug 2017341DNAArtificial
SequenceProbe sequence for murine ApoB 173ctcattctcc agcagcaggg
tttttctctt ggaaagaaag t 4117441DNAArtificial SequenceProbe sequence
for murine ApoB 174gaagcggccg tttgttgata tttttctctt ggaaagaaag t
4117541DNAArtificial SequenceProbe sequence for murine ApoB
175gtttttgctg tctgcaccca tttttctctt ggaaagaaag t
4117648DNAArtificial SequenceProbe sequence for murine ApoB
176taaatattgt ccatttttga gaagaagttt ttctcttgga aagaaagt
4817742DNAArtificial SequenceProbe sequence for murine ApoB
177cattcagctt cagtggctcc atttttctct tggaaagaaa gt
4217845DNAArtificial SequenceProbe sequence for murine ApoB
178aatgtctgca tttagcctat ggcttttttc tcttggaaag aaagt
4517944DNAArtificial SequenceProbe sequence for murine ApoB
179agcccaagct ctgcattcaa tttttaggca taggacccgt gtct
4418044DNAArtificial SequenceProbe sequence for murine ApoB
180atttcatgga tgccccagag tttttaggca taggacccgt gtct
4418148DNAArtificial SequenceProbe sequence for murine ApoB
181actgaatttt gcatggtgtt ctttttttta ggcataggac ccgtgtct
4818243DNAArtificial SequenceProbe sequence for murine ApoB
182gggcagctct cccatcaagt ttttaggcat aggacccgtg tct
4318345DNAArtificial SequenceProbe sequence for murine ApoB
183gaatcatggc ctggtaaatg ctttttaggc ataggacccg tgtct
4518448DNAArtificial SequenceProbe sequence for murine ApoB
184cagcatagga gcccatcaaa tcatttttta ggcataggac ccgtgtct
4818551DNAArtificial SequenceProbe sequence for murine ApoB
185gactgtgtgt gtggtcaagt ttcatctttt ttaggcatag gacccgtgtc t
5118650DNAArtificial SequenceProbe sequence for murine ApoB
186atagggctgt agctgtaagt taaaattttt taggcatagg acccgtgtct
5018750DNAArtificial SequenceProbe sequence for murine ApoB
187gtcaaatcta gagcaccata tctcagtttt taggcatagg acccgtgtct
5018844DNAArtificial SequenceProbe sequence for murine ApoB
188gccgaaacct tccattgttg tttttaggca taggacccgt gtct
4418953DNAArtificial SequenceProbe sequence for murine ApoB
189agatatgttt cagctcatta ttttgatagt ttttaggcat aggacccgtg tct
5319054DNAArtificial SequenceProbe sequence for murine ApoB
190ctactaccag gtcagtataa gatatggtat tttttaggca taggacccgt gtct
5419147DNAArtificial SequenceProbe sequence for murine ApoB
191gaattcgaca ccctgaacct tagtttttag gcataggacc cgtgtct
4719221DNAArtificial SequenceProbe sequence for murine ApoB
192tccccagtga cacctctgtg a 2119324DNAArtificial SequenceProbe
sequence for murine ApoB 193tcggctgagt ttgaagttga agat
2419419DNAArtificial SequenceProbe sequence for murine ApoB
194tggacagcct cagcccttc 1919525DNAArtificial SequenceProbe sequence
for murine ApoB 195tccagtgaga gacctgcaat gttca 2519626DNAArtificial
SequenceProbe sequence for murine ApoB 196tctgcttata gaacttgtct
ccactg 2619727DNAArtificial SequenceProbe sequence for murine ApoB
197gtcgttgctt aaagtagtta tgaaaga 2719822DNAArtificial SequenceProbe
sequence for murine ApoB 198gttcctttaa agttgccacc ca
2219924DNAArtificial SequenceProbe sequence for murine ApoB
199ccacagtgtc tgctctgtaa cttg 2420049DNAArtificial SequenceProbe
sequence for human ApoB 200gattggattt tcagaatact gtatagcttt
tttctcttgg aaagaaagt 4920141DNAArtificial SequenceProbe sequence
for human ApoB 201cctgcttcgt ttgctgaggt tttttctctt ggaaagaaag t
4120242DNAArtificial SequenceProbe sequence for human ApoB
202gcagtgatgg aagctgcgat atttttctct tggaaagaaa gt
4220347DNAArtificial SequenceProbe sequence for human ApoB
203gaacttctaa tttggactct cctttgtttt tctcttggaa agaaagt
4720440DNAArtificial SequenceProbe sequence for human ApoB
204actccttcag agccagcggt ttttctcttg gaaagaaagt 4020541DNAArtificial
SequenceProbe sequence for human ApoB 205actcccatgc tccgttctca
tttttctctt ggaaagaaag t 4120646DNAArtificial SequenceProbe sequence
for human ApoB 206agggtaagct gattgtttat cttgattttt ctcttggaaa
gaaagt 4620746DNAArtificial SequenceProbe sequence for human ApoB
207ggttccattc cctatgtcag catttttagg cataggaccc gtgtct
4620850DNAArtificial SequenceProbe sequence for human ApoB
208attaatctta gggtttgaga gttgtgtttt taggcatagg acccgtgtct
5020949DNAArtificial SequenceProbe sequence for human ApoB
209cactgtgttt gattttccct caatattttt aggcatagga cccgtgtct
4921051DNAArtificial SequenceProbe sequence for human ApoB
210tgtatttttt tctgtgtgta aacttgcttt ttaggcatag gacccgtgtc t
5121149DNAArtificial SequenceProbe sequence for human ApoB
211caatcactcc attactaagc tccagttttt aggcatagga cccgtgtct
4921224DNAArtificial SequenceProbe sequence for human ApoB
212tgccaaaagt aggtacttca attg 2421324DNAArtificial SequenceProbe
sequence for human ApoB 213tttgcatcta atgtgaaaag agga
2421424DNAArtificial SequenceProbe sequence for human ApoB
214catttgcttg aaaatcaaaa ttga 2421524DNAArtificial SequenceProbe
sequence for human ApoB 215ggtacttgct ggagaacttc actg
2421623DNAArtificial SequenceProbe sequence for human ApoB
216gcatttccaa aaaacagcat ttc 2321740DNAArtificial SequenceProbe
sequence for murine GAPDH 217caaatggcag ccctggtgat ttttctcttg
gaaagaaagt 4021843DNAArtificial SequenceProbe sequence for murine
GAPDH 218ccttgactgt gccgttgaat tttttttctc ttggaaagaa agt
4321941DNAArtificial SequenceProbe sequence for murine GAPDH
219gtctcgctcc tggaagatgg tttttctctt ggaaagaaag t
4122039DNAArtificial SequenceProbe sequence for murine GAPDH
220cccggccttc tccatggttt tttctcttgg aaagaaagt 3922146DNAArtificial
SequenceProbe sequence for murine GAPDH 221aacaatctcc actttgccac
tgtttttagg cataggaccc gtgtct 4622250DNAArtificial SequenceProbe
sequence for murine GAPDH 222catgtagacc atgtagttga ggtcaatttt
taggcatagg acccgtgtct 5022344DNAArtificial SequenceProbe sequence
for murine GAPDH 223gacaagcttc ccattctcgg tttttaggca taggacccgt
gtct 4422443DNAArtificial SequenceProbe sequence for murine GAPDH
224tgatgggctt cccgttgatt ttttaggcat aggacccgtg tct
4322544DNAArtificial SequenceProbe sequence for murine GAPDH
225gacatactca gcaccggcct tttttaggca taggacccgt gtct
4422619DNAArtificial SequenceProbe sequence for murine GAPDH
226tgaaggggtc gttgatggc 1922723DNAArtificial SequenceProbe sequence
for murine GAPDH 227ccgtgagtgg agtcatactg gaa 2322822DNAArtificial
SequenceProbe sequence for murine GAPDH 228caccccattt gatgttagtg gg
2222924DNAArtificial SequenceProbe sequence for murine GAPDH
229ggtgaagaca ccagtagact ccac 2423041DNAArtificial SequenceProbe
sequence for human GAPDH 230gaatttgcca tgggtggaat tttttctctt
ggaaagaaag t 4123141DNAArtificial SequenceProbe sequence for human
GAPDH 231ggagggatct cgctcctgga tttttctctt ggaaagaaag t
4123240DNAArtificial SequenceProbe sequence for human GAPDH
232ccccagcctt ctccatggtt ttttctcttg gaaagaaagt 4023340DNAArtificial
SequenceProbe sequence for human GAPDH 233gctcccccct gcaaatgagt
ttttctcttg gaaagaaagt 4023442DNAArtificial SequenceProbe sequence
for human GAPDH 234agccttgacg gtgccatgtt tttaggcata ggacccgtgt ct
4223545DNAArtificial SequenceProbe sequence for human GAPDH
235gatgacaagc ttcccgttct ctttttaggc ataggacccg tgtct
4523646DNAArtificial SequenceProbe sequence for human GAPDH
236agatggtgat gggatttcca tttttttagg cataggaccc gtgtct
4623744DNAArtificial SequenceProbe sequence for human GAPDH
237gcatcgcccc acttgatttt tttttaggca taggacccgt gtct
4423843DNAArtificial SequenceProbe sequence for human GAPDH
238cacgacgtac tcagcgccat ttttaggcat aggacccgtg tct
4323946DNAArtificial SequenceProbe sequence for human GAPDH
239ggcagagatg atgacccttt tgtttttagg cataggaccc gtgtct
4624021DNAArtificial SequenceProbe sequence for human GAPDH
240ggtgaagacg ccagtggact c 2124121RNAArtificial
SequenceSynthetically generated siRNA 241agguguaugg cuucaacccu n
2124223RNAArtificial SequenceSynthetically generated siRNA
242caggguugaa gccauacacc ucn 2324321RNAArtificial
SequenceSynthetically generated siRNA 243agguguaugg cuucaacccu n
2124423RNAArtificial SequenceSynthetically generated siRNA
244caggguugaa gccauacacc unn 2324528DNAArtificial SequenceProbe
sequence 245gattgattga cctgtccatt ctcttctt 2824628DNAArtificial
SequenceProbe sequence 246caccaacttc ttccacgagt ctcttctt
2824728DNAArtificial SequenceProbe sequence 247gagtttgtga
caaatatggg ctcttctt 2824828DNAArtificial SequenceProbe sequence
248ctttacaagc cttggttcag ttcttctt 2824921RNAArtificial
SequenceSynthetically generated siRNA 249agguguaugg cuucaacccu n
2125028DNAArtificial SequenceProbe sequence 250ggaatcttat
atttgatcca atcttctt 2825123RNAArtificial SequenceSynthetically
generated siRNA 251uuggaucaaa uauaagauuc ccn 2325221RNAArtificial
SequenceSynthetically generated siRNA 252ggaaucuuau auuugaucca
n
2125321RNAArtificial SequenceSynthetically generated siRNA
253gucaucacac ugaauaccaa n 2125423RNAArtificial
SequenceSynthetically generated siRNA 254auugguauuc agugugauga can
2325521RNAArtificial SequenceSynthetically generated siRNA
255gucaucacac ugaauaccaa n 2125623RNAArtificial
SequenceSynthetically generated siRNA 256auugguauuc agugugauga cnn
2325723RNAArtificial SequenceSynthetically generated siRNA
257uuggaucaaa uauaagauuc ccn 2325821RNAArtificial
SequenceSynthetically generated siRNA 258ggaaucuuau auuugaucca n
2125923RNAArtificial SequenceSynthetically generated siRNA
259acugaaccaa ggcuuguaaa gun 2326021RNAArtificial
SequenceSynthetically generated siRNA 260cuuuacaagc cuugguucag n
2126121RNAArtificial SequenceSynthetically generated siRNA
261gucaucacac ugaauaccaa n 2126221RNAArtificial
SequenceSynthetically generated siRNA 262cuuuacaagc cuugguucag n
2126323RNAArtificial SequenceSynthetically generated siRNA
263acugaaccaa ggcuuguaaa gun 2326423RNAArtificial
SequenceSynthetically generated siRNA 264gcccauauuu gucacaaacu ccn
2326525DNAArtificial SequenceProbe sequence 265gaactgtgtg
tgagaggtcc ttctt 2526628DNAArtificial SequenceProbe sequence
266gtgatcagac tcaatacgaa ttcttctt 2826727DNAArtificial
SequenceProbe sequence 267gtcatcacac tgaataccaa ttcttct
2726827DNAArtificial SequenceProbe sequence 268aggtgtatgg
cttcaaccct gtcttct 2726928DNAArtificial SequenceProbe sequence
269aaacaccatt gtcacactcc atcttctt 2827028DNAArtificial
SequenceProbe sequence 270gagctacagt gcttcatctc atcttctt
2827121RNAArtificial SequenceSynthetically generated
oligonucleotide 271gugaucagac ugaauacgaa n 2127223RNAArtificial
SequenceSynthetically generated oligonucleotide 272auucguauug
agucugauca can 2327321RNAArtificial SequenceSynthetically generated
oligonucleotide 273gaacugugug ugagaggucc n 2127423RNAArtificial
SequenceSynthetically generated oligonucleotide 274aggaccucuc
acacacaguu cgc 2327521RNAArtificial SequenceSynthetically generated
oligonucleotide 275gucaucacac ugaauaccaa n 2127623RNAArtificial
SequenceSynthetically generated oligonucleotide 276auugguauuc
agugugauga can 2327721RNAArtificial SequenceSynthetically generated
oligonucleotide 277gaacugugug ugagaggucc n 2127823RNAArtificial
SequenceSynthetically generated oligonucleotide 278aggaccucuc
acacacaguu cgn 2327931DNAArtificial SequencePrimer 279ctctagagcg
actggagcac gaggacactg a 3128034DNAArtificial SequencePrimer
280ctctagaggg acactgacat ggactgaagg agta 3428124DNAArtificial
SequencePrimer 281ctcctgttgc agtagagtgc agct 2428238DNAArtificial
SequencePrimer 282acgcgtcgac gtgggagcat ggaggttggc agttgttc
3828336DNAArtificial SequencePrimer 283acgcgtcgac gtaatggtgc
tgtcatgact gccctt 3628432DNAArtificial SequencePrimer 284ctctagagca
tggactgaag gagtagaaag aa 3228521RNAArtificial SequenceSynthetically
generated iRNA 285gucaucacac ugaauaccaa n 2128623RNAArtificial
SequenceSynthetically generated iRNA 286caggguugaa gccauacacc ucu
2328721RNAArtificial SequenceSynthetically generated iRNA
287gauugauuga ccuguccauu n 2128823RNAArtificial
SequenceSynthetically generated iRNA 288gaauggacag gucaaucaau cun
2328921RNAArtificial SequenceSynthetically generated iRNA
289gauugauuga ccuguccauu n 2129023RNAArtificial
SequenceSynthetically generated iRNA 290gaauggacag gucaaucaau cun
2329121RNAArtificial SequenceSynthetically generated iRNA
291caccaacuuc uuccacgagu n 2129223RNAArtificial
SequenceSynthetically generated iRNA 292gacucgugga agaaguuggu gun
2329321RNAArtificial SequenceSynthetically generated iRNA
293caccaacuuc uuccacgagu n 2129423RNAArtificial
SequenceSynthetically generated iRNA 294gacucgugga agaaguuggu gun
2329521RNAArtificial SequenceSynthetically generated iRNA
295gaguuuguga caaauauggg n 2129623RNAArtificial
SequenceSynthetically generated iRNA 296gcccauauuu gucacaaacu ccn
2329721RNAArtificial SequenceSynthetically generated iRNA
297gaguuuguga caaauauggg n 21
* * * * *